Contacts of the helix formed by residues 19 - 35 (chain B) in PDB entry 1ESG
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 ASP 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B LEU* 2.9 23.9 + - + +
16B LEU 3.8 3.7 - - - +
17B SER 3.6 0.6 - - - -
18B LYS* 1.3 78.4 - - + +
20B LYS* 1.3 57.2 + - - +
22B ILE* 3.2 27.3 + - + +
23B GLN* 2.9 28.1 + - - +
101B GLU* 2.4 37.1 - - - +
106B LYS* 2.6 33.6 + - - +
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER 4.6 12.3 + - - +
18B LYS 3.9 4.8 + - - +
19B ASP* 1.3 72.9 + - - +
21B LEU* 1.3 63.0 + - + +
23B GLN* 3.4 24.3 + - - +
24B GLN* 2.9 28.4 + - - +
101B GLU* 3.9 5.0 + - - +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ASP* 3.3 2.0 + - - -
20B LYS* 1.3 79.3 - - + +
22B ILE* 1.3 65.0 + - - +
24B GLN* 3.4 25.6 + - - +
25B ALA* 3.1 18.2 + - - +
97B LYS* 5.6 1.4 + - - +
99B PHE* 3.4 53.1 - - + -
100B ILE 4.6 3.6 - - - +
101B GLU* 3.5 30.0 + - + +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 4.0 24.9 - - + +
16B LEU* 4.3 7.9 - - + -
19B ASP* 3.2 34.6 + - + +
21B LEU* 1.3 76.0 - - - +
23B GLN* 1.3 63.3 + - - +
25B ALA* 3.2 5.3 + - - +
26B TYR* 3.1 21.3 + - - +
99B PHE* 3.3 26.9 - - + -
106B LYS* 4.3 14.6 - - + -
107B ARG 4.8 0.2 - - - +
108B VAL* 3.7 13.2 - - + -
137B ASP* 4.6 12.1 - - + -
138B LEU* 3.6 27.2 - - + +
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.4 38.9 + - + +
17B SER* 5.1 3.2 + - - +
19B ASP 2.9 14.7 + - - +
20B LYS* 3.7 30.3 + - - +
21B LEU 3.3 0.2 - - - -
22B ILE* 1.3 77.7 - - - +
24B GLN* 1.3 55.5 + - - +
26B TYR* 3.3 6.0 + - + +
27B ASN* 2.9 50.1 + - - +
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS 2.9 15.5 + - - +
21B LEU* 3.4 31.6 + - - +
22B ILE 3.2 0.2 - - - -
23B GLN* 1.3 75.1 - - - +
25B ALA* 1.3 65.7 + - - +
27B ASN* 3.1 11.9 + - + +
28B GLU* 2.9 51.2 + - + +
97B LYS* 3.7 12.6 + - - +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU 3.1 14.6 + - - +
22B ILE 3.2 8.7 + - - +
24B GLN* 1.3 76.8 - - - +
26B TYR* 1.3 63.3 + - - +
28B GLU* 3.1 12.8 + - - +
29B VAL* 3.0 19.7 + - - +
74B TRP* 3.5 24.4 - - + -
97B LYS* 4.4 12.5 - - + +
99B PHE* 4.5 1.6 - - + -
108B VAL* 3.8 25.6 - - + -
140B ILE* 5.3 0.2 - - - -
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Residues in contact with TYR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 2.5 38.8 + - - -
8B ILE* 4.0 9.4 - - + +
16B LEU* 3.7 29.8 - - + -
22B ILE 3.1 12.2 + - - +
23B GLN* 3.5 10.1 - - + +
25B ALA* 1.3 76.2 - - - +
27B ASN* 1.3 72.7 + - - +
29B VAL* 3.2 3.7 + - + +
30B LYS* 3.0 53.8 + - + +
138B LEU* 4.6 3.3 - - + +
140B ILE* 4.2 21.9 - - + +
175B ILE* 3.6 28.7 - - + -
177B ILE* 4.3 4.3 - - + -
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Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLN* 2.9 38.9 + - - +
24B GLN* 3.5 10.5 - - - +
26B TYR* 1.3 92.4 - - - +
28B GLU* 1.3 58.2 + - + +
30B LYS* 3.3 9.1 + - - +
31B THR* 2.9 33.4 + - - +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLN* 2.9 42.5 + - + +
25B ALA* 3.1 7.4 + - - +
27B ASN* 1.3 74.5 - - + +
29B VAL* 1.3 62.0 - - - +
31B THR* 3.2 7.3 + - - -
32B SER* 2.8 30.3 + - - -
68B LEU* 3.7 3.0 - - - +
72B TYR* 3.6 45.9 - - + +
74B TRP* 3.0 26.8 + - - +
97B LYS* 3.0 22.9 + - - +
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ALA 3.0 10.7 + - - +
26B TYR 3.2 7.8 + - - +
28B GLU* 1.3 77.3 - - - +
30B LYS* 1.3 62.5 + - - +
32B SER* 2.9 20.5 + - - +
33B ILE* 3.1 9.5 + - - +
68B LEU* 4.1 5.2 - - + -
74B TRP* 3.5 36.3 - - + -
110B MET* 4.5 13.5 - - + -
140B ILE* 4.0 26.0 - - + -
142B LEU* 3.8 35.2 - - + -
177B ILE* 4.3 5.6 - - + -
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 3.3 35.7 - - + +
6B GLU* 4.4 4.7 - - - +
26B TYR* 3.0 55.5 + - + +
27B ASN* 3.7 11.9 - - - +
29B VAL* 1.3 76.8 - - - +
31B THR* 1.3 63.3 + - - +
33B ILE* 3.5 7.6 - - - +
34B CYS* 3.1 38.5 + - - -
177B ILE* 4.2 11.2 - - + -
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Residues in contact with THR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASN* 2.9 21.1 + - - +
28B GLU* 3.6 5.8 - - - -
29B VAL 3.2 0.2 - - - -
30B LYS* 1.3 78.5 - - - +
32B SER* 1.3 53.3 + - - +
34B CYS* 3.4 4.0 + - - +
35B SER* 2.5 47.5 + - - +
72B TYR* 3.4 27.8 + - + +
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Residues in contact with SER 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLU 2.8 14.1 + - - -
29B VAL* 2.9 16.3 + - - +
31B THR* 1.3 80.0 - - - +
33B ILE* 1.3 56.0 + - - +
35B SER* 4.2 2.7 - - - -
36B PRO* 3.2 21.5 - - - +
64B CYS* 3.2 30.9 - - - -
67B LEU* 3.8 20.9 - - - +
68B LEU* 3.6 25.3 - - - +
72B TYR* 5.1 3.8 - - - -
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.1 20.5 - - + +
2B GLU 5.9 0.6 - - - -
3B VAL* 4.0 24.0 - - + -
29B VAL 3.1 12.8 + - - +
30B LYS* 3.5 13.0 - - - +
32B SER* 1.3 80.9 + - - +
34B CYS* 1.3 63.0 + - - +
35B SER 3.4 0.2 - - - -
36B PRO* 3.3 7.0 - - + +
60B ILE* 4.6 9.9 - - + -
64B CYS* 4.6 5.4 - - + -
112B PHE* 3.7 30.3 - - + -
142B LEU* 3.9 19.5 - - + -
177B ILE* 4.6 8.7 - - + -
179B PHE* 3.7 36.7 - - + +
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Residues in contact with CYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 3.1 40.9 + - - +
2B GLU* 4.4 1.3 - - - -
3B VAL* 3.9 32.1 - - - -
30B LYS* 3.1 28.9 + - - +
31B THR* 4.0 4.3 - - - +
33B ILE* 1.3 77.3 - - - +
35B SER* 1.3 60.9 + - - +
36B PRO* 3.3 1.3 - - - +
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B THR* 2.5 33.9 + - - +
32B SER* 4.2 0.7 - - - -
34B CYS* 1.3 78.3 - - - +
36B PRO* 1.3 71.0 - - - +
37B ILE* 3.3 14.9 + - - +
67B LEU* 4.0 14.6 - - - +
210B VAL* 3.6 28.6 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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