Contacts of the helix formed by residues 22 - 38 (chain I) in PDB entry 1VYH
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 22 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I ASP* 3.6 29.5 + - - +
20I GLY 3.3 5.8 - - - +
21I ASP* 1.3 77.9 + - - +
23I ARG* 1.3 53.3 + - - +
24I TRP 3.5 0.6 + - - -
25I MET* 3.1 36.3 + - - +
26I SER* 2.6 30.4 + - - +
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Residues in contact with ARG 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I ASP* 5.1 2.0 - - - +
19I GLN* 3.7 19.8 + - - +
21I ASP* 3.1 40.8 + - - +
22I ASP* 1.3 75.5 - - - +
24I TRP* 1.3 65.7 + - - +
26I SER* 3.5 6.3 + - - -
27I GLN* 3.0 34.7 + - - +
142J ARG* 3.7 4.6 - - - +
143J GLY* 4.1 9.6 - - - -
144J GLU 5.2 0.2 - - - +
193J ASP* 3.1 42.0 + - - +
194J PHE* 3.4 26.4 - - + -
195J LEU* 3.9 20.9 - - - +
196J HIS* 5.8 0.4 - - - -
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Residues in contact with TRP 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA* 3.9 18.2 - - + -
15I ALA* 3.9 47.2 - - + +
17I ASP* 5.8 6.8 - - + +
22I ASP* 3.5 0.8 - - - +
23I ARG* 1.3 76.9 - - - +
25I MET* 1.3 93.2 + - + +
27I GLN* 3.3 12.3 + - - +
28I HIS* 3.1 21.4 + - + +
73I ILE* 3.7 24.1 - - + +
74I GLY 5.5 1.6 - - - -
76I ASP* 2.8 24.8 + - - -
80I HIS* 4.2 13.0 - - + -
83I TRP* 3.7 26.7 - + - -
84I ARG* 3.7 25.1 - - + -
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Residues in contact with MET 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA* 5.8 1.6 - - + -
15I ALA 5.8 1.1 - - - +
22I ASP* 3.1 28.2 + - - +
24I TRP* 1.3 103.0 - - + +
26I SER* 1.3 65.2 + - - +
28I HIS* 3.7 13.6 - - + +
29I ASN* 2.9 42.6 + - - +
83I TRP* 4.2 22.0 - - + -
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Residues in contact with SER 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASP 4.5 0.9 + - - -
22I ASP* 2.6 24.7 + - - +
23I ARG* 3.5 8.6 + - - -
25I MET* 1.3 78.2 - - - +
27I GLN* 1.3 62.2 + - - +
29I ASN* 3.5 8.3 + - - +
30I ARG* 3.1 21.7 + - - +
144J GLU* 3.8 33.1 + - - +
194J PHE* 3.8 22.3 - - - -
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Residues in contact with GLN 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I ARG* 3.0 27.8 + - - +
24I TRP* 3.3 7.3 + - - +
25I MET 3.2 0.6 - - - -
26I SER* 1.3 78.1 - - - +
28I HIS* 1.3 65.5 + - - +
30I ARG* 3.1 26.1 + - - +
31I PHE* 3.1 26.5 + - + -
51I GLN* 3.7 13.5 + - - +
72I GLY 4.5 0.3 - - - +
73I ILE* 3.4 40.5 - - + +
192J PHE 4.2 0.3 - - - +
193J ASP* 3.3 33.9 + - - +
194J PHE* 4.0 16.8 - - + -
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Residues in contact with HIS 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I TRP* 3.1 14.1 + - + +
25I MET* 3.2 19.3 + - + +
27I GLN* 1.3 78.2 - - - +
29I ASN* 1.3 71.6 + - - +
31I PHE* 3.1 9.5 + - - +
32I VAL* 3.0 37.6 + - + +
73I ILE* 4.7 0.6 - - - +
83I TRP* 4.0 21.5 - + - -
84I ARG* 3.5 32.6 - - - +
87I ASN* 3.3 20.4 + - + +
89I GLU* 2.5 50.4 + - + +
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Residues in contact with ASN 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I MET* 2.9 36.9 + - - +
26I SER* 3.6 6.9 - - - +
28I HIS* 1.3 86.0 - - - +
30I ARG* 1.3 65.1 + - - +
32I VAL* 2.9 11.1 + - - +
33I LEU* 2.8 24.6 + - - +
144J GLU* 5.7 2.5 - - - +
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Residues in contact with ARG 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I SER 3.1 14.9 + - - +
27I GLN* 3.1 20.7 + - - +
29I ASN* 1.3 74.8 - - - +
31I PHE* 1.3 95.0 + - - +
33I LEU* 3.4 10.6 + - + +
34I ASP* 2.8 41.5 + - - +
51I GLN* 5.9 1.6 - - - +
54I GLN* 5.3 6.1 + - - -
70I ASN 4.5 6.5 + - - -
144J GLU* 4.9 8.5 - - - +
188J CYS* 3.6 36.8 - - - +
192J PHE 4.1 18.4 + - - -
194J PHE* 4.5 8.2 - - - -
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Residues in contact with PHE 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I GLN* 3.3 17.3 - - + -
28I HIS* 3.1 7.3 + - - +
29I ASN 3.1 0.6 - - - -
30I ARG* 1.3 116.0 - - - +
32I VAL* 1.3 54.6 + - - +
34I ASP* 2.9 10.1 + - - +
35I CYS* 2.7 38.2 + - - +
51I GLN* 5.3 1.6 - - - -
70I ASN 3.8 7.2 - - - -
71I PHE* 3.3 51.9 - + + -
72I GLY 3.7 15.5 - - - -
73I ILE* 4.0 14.8 - - + -
84I ARG* 3.8 4.5 - - - -
89I GLU* 3.4 34.8 - - - -
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Residues in contact with VAL 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I HIS* 3.0 46.6 + - + +
29I ASN* 2.9 11.4 + - - +
31I PHE* 1.3 75.3 - - - +
33I LEU* 1.3 59.1 + - - +
35I CYS* 2.8 24.7 + - + +
36I LYS* 3.0 12.2 + - + +
87I ASN 4.6 2.9 - - - +
88I GLY* 3.8 22.7 - - - +
89I GLU* 4.8 1.1 - - + -
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Residues in contact with LEU 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I ASN 2.8 15.0 + - - +
30I ARG* 3.6 9.9 - - + +
32I VAL* 1.3 77.1 - - - +
34I ASP* 1.3 64.2 + - - +
36I LYS* 3.0 26.9 + - + +
37I ASP* 3.1 21.3 - - - +
151K ASP* 3.7 33.4 - - - +
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Residues in contact with ASP 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ARG* 2.8 33.5 + - - +
31I PHE* 3.2 14.4 - - - +
33I LEU* 1.3 76.7 - - - +
35I CYS* 1.3 56.4 + - - +
37I ASP* 4.4 2.6 - - - +
38I LYS* 3.1 57.0 + - - +
69I LEU* 3.3 32.4 - - + +
71I PHE* 4.3 2.2 - - + -
93I ILE* 4.9 0.9 - - - +
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Residues in contact with CYS 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I PHE 2.7 12.0 + - - +
32I VAL* 2.8 15.4 + - + +
34I ASP* 1.3 72.8 - - - +
36I LYS* 1.3 62.7 + - - +
37I ASP 3.4 0.2 - - - -
38I LYS 4.4 2.4 - - - +
71I PHE* 3.5 28.3 - - - -
88I GLY 4.1 6.7 - - - +
89I GLU* 3.6 28.3 - - - -
91I GLU* 3.5 22.0 - - + +
92I ASN* 3.6 12.3 - - - +
93I ILE* 3.8 29.5 - - - +
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Residues in contact with LYS 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I VAL* 3.0 9.1 + - + +
33I LEU* 3.0 23.3 + - + +
35I CYS* 1.3 79.1 - - - +
37I ASP* 1.3 73.9 + - + +
92I ASN* 4.6 11.7 - - - +
151K ASP* 3.2 29.0 + - - +
170K ALA* 3.5 23.8 + - - +
172K MET* 6.3 0.4 - - - -
193K HIS* 4.2 15.5 + - + +
194K ASN* 5.5 1.9 - - - +
212K ARG* 3.1 20.1 + - - -
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Residues in contact with ASP 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I LEU* 3.1 22.4 - - - +
34I ASP* 4.1 3.3 - - - +
36I LYS* 1.3 98.3 - - + +
38I LYS* 1.3 73.3 + - - +
39I GLU* 4.7 1.9 - - - +
128K GLU* 6.2 0.4 - - - -
151K ASP* 4.0 7.6 - - - +
152K SER* 4.5 8.2 + - - -
154K GLN* 5.7 5.9 + - - +
170K ALA* 4.2 9.5 - - - +
194K ASN* 3.5 24.6 + - - +
212K ARG* 4.2 5.8 - - - +
236K TRP* 4.3 14.3 - - - -
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Residues in contact with LYS 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I ASP* 3.1 39.5 + - - +
35I CYS 4.4 1.6 - - - +
37I ASP* 1.3 90.3 + - - +
39I GLU* 1.3 65.4 + - - +
40I PRO* 4.0 4.7 - - + -
69I LEU* 4.6 22.9 - - + -
92I ASN* 5.8 0.7 - - - +
93I ILE* 4.2 12.0 + - - +
110K PRO* 4.6 7.3 - - - +
128K GLU* 3.2 35.7 + - - -
212K ARG* 4.6 6.9 + - - -
400K VAL* 5.6 3.8 - - - +
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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
------------------------------------------------------------
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