Contacts of the helix formed by residues 14 - 35 (chain A) in PDB entry 6NRB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 14 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 1.3 82.3 + - - +
15A GLU* 1.3 55.6 + - - -
16A THR 2.9 0.7 - - - -
17A ILE* 2.9 4.4 + - - +
18A ARG* 2.5 44.0 + - - +
528A ASP 3.7 16.6 + - - -
529A ASP* 5.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR 3.3 1.6 + - - -
14A GLY* 1.3 70.5 - - - -
16A THR* 1.3 52.7 + - - +
18A ARG* 2.5 44.0 + - - +
19A SER* 2.6 34.7 + - - -
105A ASP 4.6 0.2 - - - +
108A VAL* 3.3 16.7 - - - +
109A LYS* 3.3 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR 3.0 28.0 + - - +
14A GLY 2.9 0.6 - - - -
15A GLU* 1.3 75.9 - - - +
17A ILE* 1.3 52.2 + - - +
19A SER* 2.2 28.7 + - - +
20A GLN* 2.5 36.3 + - + +
23A MET* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.3 29.5 - - - +
14A GLY 2.9 21.5 + - - +
16A THR* 1.3 74.0 - - - +
18A ARG* 1.3 56.7 + - + +
20A GLN* 3.2 15.2 - - + -
21A ASN* 2.4 47.9 + - - +
69A HIS* 3.5 28.0 - - + +
528A ASP 4.3 0.9 - - - +
529A ASP* 3.8 20.9 - - - +
530A LEU* 3.5 32.3 - - + +
531A ILE* 5.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY* 2.5 27.8 + - - +
15A GLU* 2.5 49.2 + - - +
17A ILE* 1.3 74.4 - - + +
19A SER* 1.3 56.8 + - - +
21A ASN* 3.1 14.3 - - - +
22A VAL* 2.9 29.1 + - - +
108A VAL* 3.6 17.6 - - - +
109A LYS* 5.8 0.9 - - - +
524A ILE* 5.4 3.8 - - - +
525A LEU 5.3 5.7 + - - -
527A ILE 3.9 15.6 + - - +
528A ASP* 2.6 54.8 + - - +
57D MET* 4.7 5.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU 2.6 18.6 + - - -
16A THR* 2.2 34.0 + - - +
18A ARG* 1.3 72.0 - - - +
20A GLN* 1.3 51.2 + - - +
22A VAL* 2.6 12.0 + - - +
23A MET* 2.2 67.6 + - - +
105A ASP* 5.2 2.5 - - - -
109A LYS* 4.7 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 2.5 32.3 + - + +
17A ILE* 3.0 29.8 + - + +
19A SER* 1.3 72.9 + - - +
21A ASN* 1.3 60.2 - - - +
23A MET* 2.8 37.7 - - - +
24A ALA* 3.2 30.1 + - - +
69A HIS* 3.8 14.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 2.4 42.7 + - - +
18A ARG* 3.1 20.4 + - - +
19A SER 3.0 0.2 - - - -
20A GLN* 1.3 71.0 - - - +
22A VAL* 1.3 58.8 + - - +
25A ALA* 3.8 8.7 + - - +
69A HIS* 3.1 25.9 + - - -
71A ALA* 3.2 27.6 - - + +
101A LEU* 4.1 7.1 - - - +
524A ILE* 3.5 22.8 - - + +
527A ILE* 3.1 34.2 - - - +
530A LEU* 5.6 0.4 - - - +
60D MET* 4.7 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG 2.9 15.8 + - - +
19A SER* 2.6 16.3 + - - +
21A ASN* 1.3 74.1 - - + +
23A MET* 1.3 66.8 + - + +
25A ALA* 3.2 4.9 - - - +
26A ALA* 2.9 22.1 + - + +
98A ALA* 4.4 3.1 - - + +
101A LEU* 3.5 59.2 - - + +
102A LYS* 4.3 15.9 - - + -
105A ASP* 4.6 14.6 - - - +
524A ILE* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 6.2 0.4 - - + -
19A SER* 2.2 57.4 + - - +
20A GLN* 2.8 37.5 - - - +
22A VAL* 1.3 68.6 - - + +
24A ALA* 1.3 52.6 + - - +
26A ALA* 3.1 5.4 + - - +
27A SER* 2.5 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 3.2 21.6 + - - +
23A MET* 1.3 76.4 - - - +
25A ALA* 1.3 65.3 + - - +
27A SER* 3.9 7.4 - - - -
28A ILE* 2.9 29.9 + - + +
69A HIS* 3.9 28.9 - - + -
71A ALA* 4.2 5.4 - - + -
72A ALA* 4.8 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN 3.8 13.0 + - - +
22A VAL* 3.2 12.2 + - - +
23A MET 3.1 0.2 - - - -
24A ALA* 1.3 76.6 - - - +
26A ALA* 1.3 51.9 - - - +
28A ILE* 2.8 6.6 + - - +
29A ALA* 2.3 39.6 + - + +
71A ALA* 4.6 2.7 - - + +
75A LEU* 3.5 31.4 - - + +
98A ALA* 3.6 19.7 - - + -
101A LEU* 4.7 4.3 - - + -
524A ILE* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 2.9 16.7 + - + +
23A MET* 3.9 4.5 - - - +
25A ALA* 1.3 77.3 - - - +
27A SER* 1.3 58.0 + - - +
29A ALA* 3.5 10.8 - - - -
30A ASN* 2.8 27.0 + - - +
98A ALA* 3.9 3.7 - - + +
102A LYS* 4.4 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A MET* 2.5 34.7 + - - +
24A ALA* 3.5 10.5 - - - -
25A ALA 2.9 0.2 + - - -
26A ALA* 1.3 74.7 - - - +
28A ILE* 1.3 68.1 + - - -
30A ASN* 3.1 18.2 + - - +
31A ILE* 3.9 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 2.9 17.6 + - + +
25A ALA* 2.8 4.9 + - - +
27A SER* 1.3 73.4 - - - +
29A ALA* 1.3 61.1 + - - +
30A ASN 3.0 2.2 - - - -
31A ILE* 2.8 29.1 + - + +
32A VAL* 3.4 9.5 + - - +
62A LEU* 3.6 29.4 - - + -
65A LEU* 4.1 18.2 - - + -
68A GLU* 6.0 1.3 - - + +
72A ALA* 4.3 21.5 - - + -
75A LEU* 5.3 2.0 - - + -
94A VAL* 5.0 2.0 - - + -
16C ARG* 4.7 21.1 - - - +
523C VAL* 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 2.3 34.9 + - - +
26A ALA* 3.5 13.7 - - - +
28A ILE* 1.3 63.3 - - - +
30A ASN* 1.3 60.7 + - - +
31A ILE 3.3 0.2 - - - -
32A VAL* 3.1 12.2 - - - +
33A LYS* 2.8 30.6 + - - +
94A VAL* 4.0 9.8 - - + +
95A ILE* 3.4 31.3 - - + +
98A ALA* 4.6 3.1 - - + -
102A LYS* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 2.8 13.2 + - - +
27A SER* 3.1 15.2 + - - +
29A ALA* 1.3 78.4 - - - +
31A ILE* 1.3 57.8 + - + +
33A LYS* 2.9 9.6 + - - +
34A SER* 2.4 53.7 + - - -
18C SER* 4.5 9.7 + - - -
521C ASP* 3.8 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER 4.2 7.2 - - - +
28A ILE* 2.8 24.5 + - + +
30A ASN* 1.3 82.0 - - + +
32A VAL* 1.3 57.9 + - - +
34A SER* 3.2 2.9 - - - -
35A SER* 2.9 31.0 + - - -
43A LYS* 4.1 15.9 - - + -
61A ILE* 3.5 23.4 - - + +
65A LEU* 4.8 8.1 - - + -
18C SER* 4.9 3.1 - - - +
521C ASP* 3.5 25.4 - - + +
523C VAL* 3.5 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE 3.4 2.6 + - - +
29A ALA* 3.1 27.6 - - - +
31A ILE* 1.3 75.7 - - - +
33A LYS* 1.3 57.2 + - - +
35A SER 2.6 24.8 - - - +
36A LEU* 3.6 8.7 - - - +
58A GLY* 3.6 24.7 - - - +
61A ILE* 4.4 1.8 - - + -
62A LEU* 3.8 31.2 - - + -
91A THR* 3.1 33.5 + - - +
94A VAL* 3.6 8.7 - - + -
95A ILE* 3.5 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 2.8 23.0 + - - +
30A ASN* 3.5 8.7 - - - +
32A VAL* 1.3 74.9 - - - +
34A SER* 1.3 64.8 + - - +
35A SER 3.4 0.3 + - - -
36A LEU* 3.7 5.9 - - - +
95A ILE* 3.6 15.0 - - + -
447A VAL* 3.5 23.9 - - + +
450A ASN* 3.5 9.1 - - - +
451A THR* 2.9 59.7 + - - +
454A VAL* 3.4 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN* 2.4 45.9 + - - -
31A ILE* 3.2 5.4 - - - -
33A LYS* 1.3 67.6 - - - +
35A SER* 1.3 57.1 + - - +
36A LEU 3.8 0.2 - - - -
41A LEU* 3.6 4.3 + - - +
43A LYS* 2.9 20.4 + - - -
454A VAL* 3.7 15.1 - - - +
455A ASN* 3.3 16.8 + - - -
520C ASP* 6.3 1.6 - - - -
521C ASP* 2.7 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE 2.9 16.6 + - - -
32A VAL* 2.6 26.8 - - - +
34A SER* 1.3 75.4 + - - +
36A LEU* 1.3 54.3 + - - +
37A GLY 3.9 0.9 + - - -
40A GLY* 3.5 7.0 - - - -
41A LEU 3.1 12.2 + - - -
43A LYS* 3.1 27.1 - - - +
56A ASN* 3.2 20.6 - - - +
57A ASP 3.3 7.6 + - - -
58A GLY 4.0 3.6 + - - -
61A ILE* 4.9 3.1 - - - -
91A THR* 3.7 5.0 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il