Contacts of the helix formed by residues 14 - 28 (chain A) in PDB entry 4RUH
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 ASN 14 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 2.9 55.6 + - - +
11A ILE 3.6 2.5 - - - -
12A ASP 3.2 0.2 - - - -
13A GLU* 1.3 83.1 - - - +
15A GLN* 1.3 62.4 + - - +
16A ASP 3.3 3.1 - - - -
17A ARG* 3.0 39.8 + - - +
18A TYR* 3.1 38.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE 3.2 6.7 + - - +
12A ASP* 3.0 37.1 + - - +
13A GLU 3.4 2.6 - - - +
14A ASN* 1.3 76.2 - - - +
16A ASP* 1.3 63.3 + - - +
18A TYR* 3.2 15.1 - - - +
19A ILE* 3.0 30.3 + - - +
453A ARG* 2.7 39.8 + - - +
457A ILE* 3.6 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU 4.9 0.6 + - - -
14A ASN 3.3 0.6 - - - -
15A GLN* 1.3 78.9 - - - +
17A ARG* 1.3 67.0 + - - +
19A ILE* 3.2 6.9 + - - +
20A LYS* 2.9 23.8 + - - +
453A ARG* 2.6 42.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 3.1 23.8 + - - -
14A ASN* 3.0 31.1 + - + +
16A ASP* 1.3 76.0 - - - +
18A TYR* 1.3 85.1 + - - +
20A LYS* 3.1 11.3 + - + +
21A LYS* 3.0 20.9 + - + +
142A ASN* 5.5 1.0 + - - -
145A GLU* 2.8 36.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 3.5 29.1 - - - -
11A ILE* 3.4 37.5 - - + +
14A ASN* 3.1 17.0 + - + -
15A GLN* 3.2 16.6 - - - +
17A ARG* 1.3 100.9 + - - +
19A ILE* 1.3 57.4 + - - +
21A LYS* 3.0 20.9 + - + +
22A LEU 3.0 6.4 + - - -
142A ASN* 3.4 49.0 + - + +
145A GLU* 4.1 4.3 + - - -
456A TYR* 3.0 32.6 + - + +
457A ILE* 4.1 9.9 - - + -
460A THR* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN 3.0 13.7 + - - +
16A ASP* 3.2 9.6 + - - +
18A TYR* 1.3 72.1 - - - +
20A LYS* 1.3 60.8 + - - +
22A LEU* 3.2 4.5 + - - +
23A ALA* 3.0 28.7 + - + +
118A LEU* 4.1 11.0 - - + -
120A GLU* 4.2 6.5 - - - +
125A LEU* 3.8 28.0 - - + -
453A ARG* 3.3 55.0 - - + +
456A TYR* 4.1 18.2 - - + -
457A ILE* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP 2.9 13.2 + - - +
17A ARG* 3.3 13.0 - - + +
19A ILE* 1.3 76.6 - - - +
21A LYS* 1.3 60.7 + - - +
23A ALA* 4.1 6.3 - - - +
24A LYS* 3.4 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG 3.0 10.5 + - - +
18A TYR* 3.0 12.6 + - + +
20A LYS* 1.3 76.2 - - - +
22A LEU* 1.3 65.1 + - - +
24A LYS* 3.3 6.7 + - - +
25A TRP* 3.2 57.4 + - + +
47A VAL* 5.6 0.4 - - - +
51A ASP* 2.5 36.1 + - - -
138A ALA* 4.3 8.7 - - + -
141A ILE* 4.1 16.4 - - - -
142A ASN* 3.3 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR 3.0 11.2 + - - +
19A ILE* 3.2 8.0 + - - +
21A LYS* 1.3 79.0 - - - +
23A ALA* 1.3 57.1 + - - +
25A TRP* 3.1 6.8 + - + +
26A VAL* 2.8 46.3 + - + +
118A LEU* 4.0 14.6 - - + -
125A LEU* 4.0 26.9 - - + -
130A SER* 4.1 12.6 - - - +
134A LYS* 3.7 11.4 - - + +
135A GLY* 3.4 40.4 - - - +
138A ALA* 5.1 2.2 - - + -
451A LEU* 4.5 2.7 - - + -
456A TYR* 4.0 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.0 13.9 + - + +
20A LYS* 4.1 7.2 - - - +
21A LYS 3.4 0.2 - - - -
22A LEU* 1.3 75.5 - - - +
24A LYS* 1.3 56.6 + - - +
26A VAL* 3.2 2.6 + - - +
27A ALA* 3.0 29.3 + - - +
116A PHE 4.7 1.0 - - - +
117A THR* 5.8 0.2 - - - -
118A LEU* 3.4 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS 3.4 11.2 + - - +
21A LYS* 3.3 10.7 + - - +
22A LEU 3.3 0.4 - - - -
23A ALA* 1.3 75.7 - - - +
25A TRP* 1.3 68.7 + - + +
27A ALA* 3.6 15.2 + - + +
28A ILE* 3.5 30.5 - - + +
47A VAL* 6.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 3.2 42.3 + - + +
22A LEU* 3.1 9.2 + - + +
24A LYS* 1.3 79.8 - - + +
26A VAL* 1.3 58.5 + - - +
27A ALA 3.1 0.4 - - - -
28A ILE* 3.2 11.8 + - + +
44A MET* 3.5 29.7 - - + +
47A VAL* 3.7 17.5 - - + +
48A ALA* 4.6 15.9 - - + -
51A ASP* 3.4 21.3 - - - -
100A LEU* 4.0 8.3 - - + -
134A LYS* 2.6 62.3 + - + -
137A VAL* 3.7 19.7 - - + -
138A ALA* 3.6 33.9 - - + -
141A ILE* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 2.8 40.7 + - + +
23A ALA* 3.2 8.5 + - - +
25A TRP* 1.3 77.2 - - - +
27A ALA* 1.3 61.8 + - - +
28A ILE 3.4 2.8 + - - +
115A PRO 4.0 8.1 - - - +
116A PHE* 3.5 36.9 - - - +
118A LEU* 4.0 26.0 - - + +
127A GLY* 4.4 5.8 - - - -
128A ARG 3.9 16.1 - - - +
129A GLY 4.7 1.8 - - - -
130A SER 4.5 11.7 - - - +
134A LYS* 4.1 9.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 3.0 15.2 + - - +
24A LYS* 3.7 18.2 - - + +
25A TRP 3.1 0.4 - - - -
26A VAL* 1.3 79.3 - - - +
28A ILE* 1.3 60.4 + - + +
29A GLN* 3.2 17.3 + - - +
116A PHE* 3.2 18.6 - - - +
117A THR* 5.8 0.4 - - - -
----------------------------------------------------------
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 LYS* 3.5 31.2 - - + +
25A TRP* 3.2 7.9 + - + +
26A VAL 4.0 1.8 - - - +
27A ALA* 1.3 75.3 - - + +
29A GLN* 1.3 54.5 + - - +
30A SER 2.6 17.5 + - - +
40A GLU* 3.4 31.4 - - + +
43A ARG* 4.8 7.9 - - + -
44A MET* 3.8 27.6 - - + +
47A VAL* 3.7 30.3 - - + -
116A PHE* 5.0 0.2 - - - -
134A LYS* 2.7 23.2 + - - -
----------------------------------------------------------
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