Contacts of the helix formed by residues 18 - 35 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PRO* 3.7 17.2 + - - +
15A ASP* 2.8 37.6 + - - -
17A ASN* 1.3 82.5 - - - +
19A GLN* 1.3 64.5 + - - +
20A GLU* 3.6 13.7 + - - +
21A TYR* 3.1 17.7 + - - +
22A ARG* 3.1 23.1 + - - +
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Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASN 3.9 0.6 + - - +
18A SER* 1.3 74.3 - - - +
20A GLU* 1.3 72.5 + - - +
22A ARG* 3.9 9.2 - - - +
23A SER* 3.0 25.3 + - - -
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 3.5 22.3 - - + +
12A THR* 3.7 32.8 - - + +
18A SER* 3.6 10.7 - - - +
19A GLN* 1.3 84.4 + - - +
21A TYR* 1.3 61.6 + - - +
23A SER* 3.4 15.7 - - - -
24A ARG* 3.4 16.0 + - - +
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Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO 3.7 5.2 - - - -
12A THR 3.1 22.0 + - - +
13A TYR* 3.4 15.0 - - - -
15A ASP 3.2 32.5 - - - +
16A ILE* 3.7 12.8 - - + +
18A SER* 3.1 5.8 + - - +
20A GLU* 1.3 76.9 - - - +
22A ARG* 1.3 66.1 + - - +
24A ARG* 3.1 14.6 + - - +
25A ILE* 3.1 35.0 + - + +
49A VAL* 3.2 31.1 + - + +
50A GLY 4.1 1.9 + - - -
51A GLY* 3.0 38.7 + - - -
52A PHE* 4.5 3.3 + + - -
302A SAM 3.2 19.6 + - - -
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Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE 3.9 11.1 + - - +
17A ASN* 3.5 40.7 + - - +
18A SER 3.1 21.9 + - - +
19A GLN* 3.9 8.3 - - - +
21A TYR* 1.3 75.6 - - - +
23A SER* 1.3 57.4 + - - +
25A ILE* 3.2 11.8 + - + +
26A GLU* 2.9 48.9 + - + +
83A ARG* 5.7 1.2 - - - +
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Residues in contact with SER 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLN 3.0 18.0 + - - -
20A GLU* 3.4 8.3 - - - -
21A TYR 3.2 0.2 - - - -
22A ARG* 1.3 78.9 - - - +
24A ARG* 1.3 61.8 + - - +
26A GLU* 3.6 7.6 + - - +
27A THR* 2.9 34.7 + - - -
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 2.8 53.8 + - + -
13A TYR* 3.3 19.7 - - - -
20A GLU 3.5 10.1 - - - +
21A TYR* 3.1 25.4 + - - +
23A SER* 1.3 75.4 - - - +
25A ILE* 1.3 64.7 + - - +
27A THR* 3.4 4.7 + - - -
28A LEU* 3.1 30.7 + - + +
52A PHE* 3.8 14.5 - - + -
111A ASP* 3.2 25.9 + - - +
302A SAM 2.4 42.4 + - - -
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.9 9.6 - - + +
21A TYR* 3.1 36.4 + - + +
22A ARG* 3.2 13.7 + - + +
24A ARG* 1.3 76.7 - - - +
26A GLU* 1.3 59.9 + - + +
27A THR 3.1 0.3 + - - -
28A LEU* 3.2 1.6 + - - +
29A GLU* 2.7 45.2 + - - +
51A GLY* 4.1 17.7 - - - +
52A PHE* 3.7 23.4 - - + -
55A LEU* 3.8 28.7 - - + -
83A ARG* 6.1 1.6 - - - +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 2.9 36.5 + - + +
23A SER* 4.3 5.3 - - - +
25A ILE* 1.3 77.9 - - + +
27A THR* 1.3 61.9 + - - +
29A GLU* 4.2 12.6 - - - +
30A PRO* 3.3 17.3 - - - +
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A SER* 2.9 26.7 + - - -
24A ARG* 3.7 6.3 - - - -
25A ILE 3.1 0.2 - - - -
26A GLU* 1.3 79.2 - - - +
28A LEU* 1.3 67.7 + - + +
30A PRO* 3.5 14.4 - - - +
31A LEU* 3.9 10.2 - - + +
141A TYR* 6.0 0.4 - - + +
215A VAL* 4.0 26.9 - - + -
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.1 15.0 + - + +
27A THR* 1.3 87.5 - - + +
29A GLU* 1.3 66.2 + - - +
30A PRO 3.3 0.7 - - - -
31A LEU* 2.9 31.7 + - + +
32A LEU* 2.9 21.7 + - + +
52A PHE* 3.9 28.5 - - + -
110A ILE* 3.9 29.4 - - + -
111A ASP* 5.2 1.1 - - - +
141A TYR* 3.8 42.0 - - + -
215A VAL* 4.8 0.4 - - + -
221A LEU* 4.5 10.1 - - + -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 2.7 29.4 + - - +
26A GLU* 4.2 11.3 - - - +
28A LEU* 1.3 70.2 - - - +
30A PRO* 1.3 70.5 - - + +
32A LEU* 3.2 6.1 + - - +
33A MSE 3.1 28.4 + - + +
55A LEU* 3.8 32.1 - - + +
59A TYR* 2.6 37.2 + - + +
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Residues in contact with PRO 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU 3.3 16.8 - - - +
27A THR 3.5 12.3 - - - +
28A LEU 3.4 1.6 - - - -
29A GLU* 1.3 97.4 - - + +
31A LEU* 1.3 69.9 + - + +
33A MSE 3.5 7.0 + - + +
34A LYS* 3.2 21.1 + - - +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 3.9 19.1 - - + +
28A LEU* 2.9 14.2 + - + +
30A PRO* 1.3 81.7 - - + +
32A LEU* 1.3 64.5 + - - +
34A LYS* 3.3 17.3 + - + +
35A TYR* 3.4 22.4 - - - -
213A GLU* 4.4 24.9 - - + +
215A VAL* 3.8 30.1 - - + -
221A LEU* 3.4 26.0 - - + +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 2.9 26.0 + - + +
29A GLU* 3.2 7.4 + - - +
31A LEU* 1.3 76.6 - - - +
33A MSE 1.3 76.8 + - + +
35A TYR* 3.5 3.4 + - - -
36A MSE 3.0 44.7 + - - +
52A PHE* 4.1 27.1 - - + -
55A LEU* 4.8 4.9 - - + -
56A LEU* 4.9 9.4 - - + -
108A ILE* 5.0 8.3 - - + -
110A ILE* 4.6 11.9 - - + -
139A ILE* 3.8 29.8 - - + -
221A LEU* 4.2 12.3 - - + -
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Residues in contact with MSE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU* 3.1 17.2 + - + +
30A PRO* 4.0 6.7 - - + +
31A LEU 3.3 0.2 - - - -
32A LEU* 1.3 99.2 - - + +
34A LYS* 1.3 64.7 + - - +
35A TYR 3.1 3.2 + - - -
36A MSE 3.5 13.5 + - + +
37A LYS* 3.8 17.7 + - - +
39A ARG* 3.9 25.1 - - - -
55A LEU* 5.5 2.5 - - + -
56A LEU* 3.6 26.7 - - + -
59A TYR* 3.9 42.8 - - + +
61A PHE* 4.5 1.6 - - - -
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PRO 3.2 13.8 + - - +
31A LEU* 3.4 17.7 - - + +
32A LEU 3.2 0.6 - - - -
33A MSE 1.3 77.0 - - - +
35A TYR* 1.3 82.2 + - + +
37A LYS* 2.8 29.3 + - - +
213A GLU* 3.1 32.1 + - - +
133B LYS* 5.3 13.9 - - - +
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Residues in contact with TYR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.4 22.2 - - - +
32A LEU 3.5 2.9 + - - +
34A LYS* 1.3 106.0 - - + +
36A MSE 1.3 62.4 + - - +
37A LYS* 3.6 3.6 - - - -
106A TYR* 3.7 3.3 + - - -
137A LYS* 2.7 34.6 + - - +
139A ILE* 4.3 9.8 - - + +
210A GLU* 4.3 13.2 - - + -
211A ALA* 3.4 28.9 - - + +
212A GLU 4.6 0.7 + - - -
213A GLU* 2.5 42.0 + - + +
221A LEU* 4.4 5.6 - - + -
223A VAL* 3.5 31.2 - - + -
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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
------------------------------------------------------------
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