Contacts of the helix formed by residues 18 - 35 (chain B) in PDB entry 1VE3
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 18 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PRO* 3.4 15.0 + - - -
15B ASP* 2.7 42.8 + - - -
16B ILE 3.3 0.2 - - - -
17B ASN* 1.3 78.3 - - - +
19B GLN* 1.3 65.4 + - - +
20B GLU* 3.7 11.9 + - - -
21B TYR* 3.0 17.7 + - - +
22B ARG* 2.9 26.3 + - - +
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Residues in contact with GLN 19 (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 ASN 3.9 1.7 + - - +
18B SER* 1.3 72.4 - - - +
20B GLU* 1.3 70.4 + - - +
22B ARG* 3.8 13.0 - - - +
23B SER* 2.9 25.0 + - - -
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 3.9 14.0 - - + +
12B THR* 3.9 32.7 - - + +
18B SER* 3.8 10.8 - - - +
19B GLN* 1.3 86.2 + - - +
21B TYR* 1.3 62.8 + - - +
23B SER* 3.2 15.7 + - - -
24B ARG* 3.3 17.6 + - - +
151B ARG* 5.4 0.2 + - - -
155B SER* 4.2 18.8 + - - +
158B VAL* 5.0 15.1 - - - +
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Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B THR 3.2 24.8 + - - +
13B TYR* 3.5 24.5 - - - -
15B ASP 3.0 33.9 - - - +
16B ILE* 3.6 14.4 - - + -
18B SER* 3.0 9.0 + - - +
20B GLU* 1.3 75.4 - - - +
22B ARG* 1.3 63.9 + - - +
24B ARG* 3.0 22.3 + - - +
25B ILE* 3.0 37.5 + - + +
47B CYS 4.6 0.5 + - - -
49B VAL* 3.6 17.6 + - + +
50B GLY 4.2 2.1 + - - -
51B GLY* 3.1 28.9 + - - -
52B PHE* 4.3 4.8 + + - -
301B SAM 3.2 19.1 + - - -
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Residues in contact with ARG 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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16B ILE 4.1 9.8 + - - +
17B ASN* 3.4 37.5 + - - +
18B SER 2.9 21.3 + - - +
19B GLN* 3.8 11.7 - - - +
21B TYR* 1.3 76.3 - - - +
23B SER* 1.3 57.2 + - - +
25B ILE* 3.0 12.9 + - + +
26B GLU* 2.8 45.2 + - + +
83B ARG* 5.8 4.0 - - - +
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Residues in contact with SER 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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19B GLN 2.9 13.5 + - - -
20B GLU* 3.3 12.6 - - - -
21B TYR 3.1 0.2 - - - -
22B ARG* 1.3 77.5 - - - +
24B ARG* 1.3 57.5 + - - +
26B GLU* 3.9 7.9 - - - +
27B THR* 2.7 39.3 + - - -
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Residues in contact with ARG 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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12B THR* 3.0 46.6 + - - -
13B TYR* 3.5 13.1 - - - +
20B GLU 3.3 8.9 + - - +
21B TYR* 3.0 23.1 + - - +
23B SER* 1.3 76.9 - - - +
25B ILE* 1.3 64.0 + - - +
27B THR* 3.3 5.8 + - - -
28B LEU* 3.1 30.6 + - + +
52B PHE* 3.6 14.3 - - + -
111B ASP* 2.8 32.5 + - - +
151B ARG* 3.5 22.0 - - - +
301B SAM 2.4 44.5 + - - -
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Residues in contact with ILE 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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16B ILE* 4.8 9.4 - - + +
21B TYR* 3.0 41.5 + - + +
22B ARG* 3.0 15.3 + - + +
24B ARG* 1.3 76.5 - - - +
26B GLU* 1.3 62.6 + - + +
28B LEU* 3.7 0.9 - - - +
29B GLU* 2.8 34.0 + - - +
51B GLY* 4.2 17.5 - - - +
52B PHE* 3.9 20.6 - - + -
55B LEU* 4.0 30.1 - - + -
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Residues in contact with GLU 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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22B ARG* 2.8 34.2 + - + +
23B SER* 4.1 5.8 - - - +
25B ILE* 1.3 77.0 - - + +
27B THR* 1.3 62.5 + - - +
29B GLU* 4.0 15.5 - - - +
30B PRO* 3.3 18.5 - - - +
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 2.7 28.0 + - - -
24B ARG* 3.7 6.7 - - - -
25B ILE 3.2 0.2 - - - -
26B GLU* 1.3 78.5 - - - +
28B LEU* 1.3 66.1 + - + +
30B PRO* 3.9 7.3 - - - +
31B LEU* 3.5 15.6 - - + +
215B VAL* 3.7 29.4 - - + -
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Residues in contact with LEU 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 ARG* 3.1 15.4 + - + +
27B THR* 1.3 90.9 - - + +
29B GLU* 1.3 65.7 + - - +
30B PRO* 3.3 1.8 - - - -
31B LEU* 3.0 13.7 + - + +
32B LEU* 3.0 32.4 + - + +
52B PHE* 3.9 21.5 - - + -
110B ILE* 3.6 36.3 - - + -
111B ASP* 5.1 1.3 - - - +
141B TYR* 3.9 40.4 - - + -
215B VAL* 4.6 1.3 - - + -
221B LEU* 4.2 14.4 - - + -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 2.8 25.2 + - - +
26B GLU* 4.0 17.8 - - - +
28B LEU* 1.3 72.8 - - - +
30B PRO* 1.3 70.0 - - + +
32B LEU* 3.4 4.2 + - - +
33B MSE 3.2 28.4 + - + +
55B LEU* 3.8 31.9 - - + +
59B TYR* 2.5 36.4 + - + +
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Residues in contact with PRO 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU 3.3 15.0 - - - +
27B THR 3.9 9.4 - - - +
28B LEU 3.5 1.8 - - - -
29B GLU* 1.3 96.1 - - + +
31B LEU* 1.3 71.7 + - + +
33B MSE 3.4 5.3 + - + +
34B LYS* 3.1 24.8 + - - +
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Residues in contact with LEU 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 THR* 3.5 21.3 - - + +
28B LEU* 3.0 12.5 + - + +
30B PRO* 1.3 83.2 - - + +
32B LEU* 1.3 61.9 + - - +
34B LYS* 3.5 11.9 + - + +
35B TYR* 3.1 27.8 - - - -
213B GLU* 3.8 32.1 - - + +
214B LYS 5.6 1.8 - - - +
215B VAL* 3.8 29.6 - - + -
221B LEU* 3.9 21.5 - - + +
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Residues in contact with LEU 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 LEU* 3.0 27.8 + - + +
29B GLU* 3.8 2.9 - - - +
31B LEU* 1.3 78.0 - - - +
33B MSE 1.3 74.9 + - + +
35B TYR* 3.1 4.3 + - - +
36B MSE 3.0 42.1 + - - +
52B PHE* 4.2 24.9 - - + -
55B LEU* 4.8 9.0 - - + -
56B LEU* 5.0 7.6 - - + -
108B ILE* 4.6 11.9 - - + -
110B ILE* 4.4 11.2 - - + -
139B ILE* 3.7 30.7 - - + -
221B LEU* 4.0 12.1 - - + -
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Residues in contact with MSE 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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29B GLU* 3.2 17.0 + - + +
30B PRO* 3.4 5.4 + - + +
32B LEU* 1.3 98.5 - - + +
34B LYS* 1.3 63.4 + - - +
35B TYR 3.1 0.6 + - - -
36B MSE 3.6 28.3 + - + +
37B LYS* 3.6 22.3 + - - +
39B ARG* 5.0 6.5 - - - +
55B LEU* 5.9 2.2 - - + -
56B LEU* 3.7 16.2 - - + -
59B TYR* 4.1 46.2 - - + +
61B PHE* 4.1 14.1 - - - -
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Residues in contact with LYS 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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30B PRO 3.1 17.4 + - - +
31B LEU* 3.7 12.3 - - + +
32B LEU 3.1 0.4 - - - -
33B MSE 1.3 78.4 - - - +
35B TYR* 1.3 85.7 + - + +
36B MSE 3.6 0.2 - - - -
37B LYS* 3.8 27.9 - - - +
213B GLU* 3.2 25.3 + - - +
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Residues in contact with TYR 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 LEU* 3.1 22.0 - - - -
32B LEU* 3.1 6.3 + - - +
34B LYS* 1.3 105.9 + - + +
36B MSE 1.3 60.6 + - - +
37B LYS* 3.6 2.9 - - - -
106B TYR* 3.7 1.2 - - - -
137B LYS* 2.7 35.4 + - - +
139B ILE* 4.3 9.6 - - + +
210B GLU* 3.9 18.2 - - - -
211B ALA* 3.3 32.0 - - + +
212B GLU 4.1 0.3 + - - -
213B GLU* 2.6 44.0 + - + +
221B LEU* 4.2 6.1 - - + -
223B VAL* 3.6 25.8 - - + -
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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