Contacts of the helix formed by residues 13 - 29 (chain A) in PDB entry 3RNT
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 SER 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 2.8 30.8 + - - +
4A TYR* 4.6 8.0 + - - -
12A SER* 1.3 72.7 - - - +
14A SER* 1.3 63.3 + - - +
16A VAL* 3.2 10.1 + - - +
17A SER* 2.9 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 2.8 21.6 + - - -
13A SER* 1.3 80.3 - - - +
15A ASP* 1.4 61.6 + - - +
17A SER* 3.8 7.6 - - - -
18A THR* 3.0 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A CYS 4.2 0.5 - - - +
11A TYR* 3.5 26.7 - - + -
12A SER* 2.9 34.9 + - - +
14A SER* 1.4 81.8 + - - +
16A VAL* 1.3 63.6 + - - +
18A THR* 3.9 4.8 - - - -
19A ALA* 3.2 24.9 + - - +
61A ILE* 3.7 6.2 - - + +
65A GLY* 4.4 15.2 - - - +
105A CA 2.3 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.6 33.2 - - + -
11A TYR* 4.3 4.9 - - + -
12A SER 3.2 6.7 + - - +
13A SER* 3.2 7.3 + - - +
15A ASP* 1.3 75.7 - - - +
17A SER* 1.3 59.8 + - - +
19A ALA* 3.9 1.0 - - - +
20A GLN* 2.9 31.3 + - - +
61A ILE* 3.8 20.6 - - + -
78A VAL* 4.3 6.0 - - + +
86A LEU* 3.8 41.3 - - + -
89A VAL* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 2.9 17.6 + - - -
14A SER* 3.8 9.2 - - - -
16A VAL* 1.3 77.9 - - - +
18A THR* 1.3 61.5 + - - +
20A GLN* 3.4 9.2 + - - +
21A ALA* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 3.0 19.6 + - - -
15A ASP* 3.9 5.2 - - - -
17A SER* 1.3 73.1 - - - +
19A ALA* 1.3 65.3 + - - +
21A ALA* 3.4 6.2 + - - +
22A ALA* 3.3 21.0 + - - +
65A GLY 5.3 6.1 - - - +
67A VAL* 3.6 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP 3.2 15.6 + - - +
16A VAL 3.9 2.2 - - - +
18A THR* 1.3 78.8 - - - +
20A GLN* 1.3 65.7 + - - +
22A ALA* 3.3 4.3 + - - +
23A GLY 2.9 18.2 + - - -
59A TRP* 3.1 24.1 + - + +
60A PRO 4.4 0.4 - - - +
61A ILE* 4.0 31.2 - - + -
67A VAL* 4.9 7.4 - - + +
78A VAL* 4.2 5.4 - - + -
----------------------------------------------------------
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 VAL* 2.9 19.0 + - - +
17A SER* 3.8 8.4 - - - +
19A ALA* 1.3 77.0 - - - +
21A ALA* 1.3 53.7 + - - +
23A GLY 3.2 0.8 + - - +
24A TYR* 2.8 33.6 + - - +
59A TRP* 5.0 0.9 - - - -
78A VAL* 4.0 14.7 - - + +
80A PHE* 3.9 24.1 - - + +
84A ASN* 2.9 48.7 + - - +
85A GLN 3.8 1.0 - - - -
86A LEU* 3.5 34.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER 3.1 17.4 + - - +
18A THR* 3.8 6.1 - - - +
19A ALA 3.3 0.4 - - - -
20A GLN* 1.3 77.7 - - - +
22A ALA* 1.3 61.2 + - - +
24A TYR* 4.0 5.0 - - - +
25A LYS* 3.1 25.3 + - - +
84A ASN* 5.2 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR 3.3 10.6 + - - +
19A ALA 3.7 6.7 - - - +
20A GLN 3.2 0.2 - - - -
21A ALA* 1.3 76.0 - - - +
23A GLY* 1.4 64.8 + - - +
25A LYS* 3.2 39.9 + - - +
26A LEU* 3.3 10.4 + - - +
59A TRP* 4.2 5.8 - - + +
67A VAL* 3.5 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 2.9 12.1 + - - -
20A GLN 3.2 2.0 + - - -
22A ALA* 1.4 75.0 - - - +
24A TYR* 1.3 56.8 + - - +
26A LEU* 3.2 2.3 + - - +
27A HIS* 3.0 23.9 + - - +
39A PRO* 3.5 11.1 - - - +
59A TRP* 3.6 34.0 - - - +
80A PHE* 3.6 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN 2.8 12.9 + - - +
21A ALA* 4.0 4.3 - - - +
23A GLY* 1.3 73.8 - - - +
25A LYS* 1.3 59.5 + - - +
27A HIS* 3.1 21.0 + + - +
28A GLU* 2.9 63.9 + - + +
80A PHE* 3.6 24.9 - + + -
81A ASN 3.5 9.9 - - - -
82A GLU* 2.6 30.5 + - - -
83A ASN* 4.6 0.5 - - - -
84A ASN* 3.3 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA 3.1 13.3 + - - +
22A ALA* 3.2 40.6 + - - +
23A GLY 3.4 0.2 - - - -
24A TYR* 1.3 77.8 - - - +
26A LEU* 1.3 90.4 + - - +
28A GLU* 3.3 16.5 + - - +
29A ASP* 3.0 38.5 + - - +
59A TRP* 5.4 0.2 - - - -
67A VAL* 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 3.3 19.9 + - - +
23A GLY 3.2 7.2 + - - +
25A LYS* 1.3 103.3 - - + +
27A HIS* 1.3 64.2 + - - +
29A ASP* 3.1 8.9 + - - +
30A GLY 3.0 4.5 + - - -
31A GLU* 2.9 57.6 + - + +
32A THR* 5.0 2.0 - - - +
33A VAL* 4.7 13.2 - - + -
39A PRO* 3.6 7.6 - - + -
59A TRP* 3.4 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 3.0 13.4 + - - +
24A TYR* 3.1 38.6 + + - +
26A LEU* 1.3 78.4 - - - +
28A GLU* 1.3 62.4 + - + +
30A GLY* 3.4 11.4 + - - -
31A GLU 4.8 1.3 - - - +
39A PRO* 4.0 13.7 - - + +
57A TYR* 3.4 42.0 - + - -
80A PHE* 4.3 9.0 - + + -
82A GLU* 2.6 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 2.9 51.3 + - + +
25A LYS* 3.6 21.0 - - - +
27A HIS* 1.3 77.8 - - + +
29A ASP* 1.3 67.8 + - - +
30A GLY* 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 3.0 31.8 + - - +
26A LEU* 3.6 11.9 - - - +
28A GLU* 1.3 88.6 - - - +
30A GLY* 1.3 60.0 + - - +
31A GLU* 4.3 15.2 - - + +
----------------------------------------------------------
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