Contacts of the helix formed by residues 22 - 35 (chain K) in PDB entry 6VEN
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 THR 22 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20K SER 4.7 4.7 - - - +
21K ASP* 1.3 76.9 - - - +
23K ILE* 1.3 63.2 + - - +
24K GLU* 3.3 12.5 + - - +
25K ASN* 3.0 27.4 + - + +
26K VAL* 3.0 20.4 + - - +
53K GLY 5.6 1.3 - - - -
54K ARG 4.6 3.1 - - - -
55K THR* 4.1 25.8 - - + +
56K LEU 4.0 0.4 - - - -
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Residues in contact with ILE 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K THR* 1.3 74.1 - - - +
24K GLU* 1.3 62.0 + - + +
26K VAL* 2.9 13.6 + - + +
27K LYS* 2.8 58.6 + - - +
43K LEU* 6.0 1.6 - - + -
50K LEU* 4.4 14.8 - - + +
51K GLU 3.0 27.1 - - - +
52K ASP* 3.2 21.3 - - - +
54K ARG 3.1 24.3 + - - +
55K THR 3.4 20.9 - - - +
56K LEU* 3.5 10.7 - - + +
59K TYR* 4.5 12.6 - - + -
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Residues in contact with GLU 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K THR* 3.1 10.9 + - - +
23K ILE* 1.3 85.8 - - + +
25K ASN* 1.3 56.1 + - - +
27K LYS* 3.3 27.1 + - - +
28K ALA* 2.9 28.1 + - - +
38K PRO* 5.1 5.0 - - - +
52K ASP* 3.0 33.3 - - - +
53K GLY* 5.6 3.8 - - - +
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Residues in contact with ASN 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K VAL* 4.9 1.0 - - - +
21K ASP* 3.2 36.3 + - - +
22K THR* 3.0 30.3 + - + +
24K GLU* 1.3 75.3 - - - +
26K VAL* 1.3 56.7 + - - +
28K ALA* 3.3 8.5 + - - +
29K LYS* 2.9 51.5 + - - +
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Residues in contact with VAL 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K LEU* 4.5 7.2 - - + -
17K VAL* 4.3 14.4 - - + -
21K ASP* 4.9 3.1 - - + -
22K THR 3.0 13.0 + - - +
23K ILE* 2.9 11.9 + - + +
25K ASN* 1.3 75.3 - - - +
27K LYS* 1.3 60.6 + - - +
29K LYS* 3.2 7.6 + - - +
30K ILE* 2.9 51.1 + - + +
43K LEU* 4.3 17.3 - - + -
56K LEU* 4.0 37.9 - - + -
67K LEU* 6.1 2.7 - - + -
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Residues in contact with LYS 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K ILE* 2.8 41.8 + - - +
24K GLU* 3.6 28.5 - - - +
26K VAL* 1.3 76.5 - - + +
28K ALA* 1.3 57.8 + - - +
30K ILE* 3.3 11.2 + - + +
31K GLN* 3.0 28.1 + - - +
36K ILE 4.8 0.5 - - - +
38K PRO* 3.6 27.7 - - + +
41K GLN* 3.4 40.0 + - - +
43K LEU* 4.4 19.6 - - + +
50K LEU* 5.0 5.9 + - - +
52K ASP* 4.4 12.6 - - - -
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Residues in contact with ALA 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K GLU 2.9 16.5 + - - +
25K ASN* 3.5 11.7 - - - +
27K LYS* 1.3 78.3 - - - +
29K LYS* 1.3 53.1 + - + +
31K GLN* 3.3 12.3 + - - +
32K ASP* 2.7 39.1 + - - +
38K PRO* 4.2 6.9 - - + +
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Residues in contact with LYS 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LEU* 3.7 23.0 - - + +
16K GLU 4.7 10.8 - - - +
17K VAL* 4.6 9.9 - - + -
21K ASP* 5.5 1.6 - - - -
25K ASN* 2.9 43.0 + - - +
26K VAL* 3.5 6.1 - - - +
28K ALA* 1.3 73.6 - - + +
30K ILE* 1.3 63.5 + - - +
32K ASP* 2.7 35.1 + - - +
33K LYS* 2.9 13.2 + - - +
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Residues in contact with ILE 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K VAL* 4.0 17.7 - - + -
13K ILE* 6.1 2.5 - - + -
15K LEU* 3.2 20.6 - - + -
26K VAL* 2.9 34.6 + - + +
27K LYS* 3.8 8.5 - - + +
28K ALA 3.3 0.2 - - - -
29K LYS* 1.3 74.7 - - - +
31K GLN* 1.3 56.9 + - - +
33K LYS* 4.0 1.7 - - - +
34K GLU* 2.9 36.8 + - + +
35K GLY 3.9 0.2 + - - -
36K ILE* 3.9 15.6 - - + +
41K GLN* 5.3 4.9 - - + +
43K LEU* 4.0 17.3 - - + -
69K LEU* 3.9 33.9 - - + -
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Residues in contact with GLN 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K LYS 3.0 13.1 + - - +
28K ALA* 3.4 14.0 + - - +
30K ILE* 1.3 76.1 - - - +
32K ASP* 1.3 64.1 + - - +
34K GLU 2.9 0.2 + - - -
35K GLY* 2.3 40.6 + - - +
36K ILE 3.1 27.9 + - - +
37K PRO* 3.6 12.3 - - - +
38K PRO* 3.3 27.7 - - + +
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Residues in contact with ASP 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LEU* 5.3 0.3 - - - +
28K ALA* 2.7 29.8 + - - +
29K LYS* 2.7 45.2 + - - +
31K GLN* 1.3 75.6 - - - +
33K LYS* 1.3 61.9 + - - +
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Residues in contact with LYS 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K ILE* 4.3 18.8 - - + -
14K THR 6.1 0.9 - - - -
15K LEU* 4.3 13.9 - - + -
29K LYS 2.9 14.8 + - - +
30K ILE* 4.0 3.1 - - - +
32K ASP* 1.3 85.8 + - - +
34K GLU* 1.3 79.5 + - + +
35K GLY 3.8 0.2 - - - -
927N LEU* 5.6 1.0 - - - +
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Residues in contact with GLU 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K LYS* 5.8 1.2 - - - -
13K ILE* 4.1 21.1 - - + +
30K ILE* 2.9 18.6 + - + +
33K LYS* 1.3 98.6 - - + +
35K GLY* 1.3 62.4 + - - +
36K ILE* 3.4 9.7 + - + +
921N ILE* 3.6 26.2 - - - +
927N LEU* 3.3 26.3 - - - +
928N LEU* 3.1 49.6 - - + +
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Residues in contact with GLY 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K GLN* 2.3 35.5 + - - +
32K ASP 4.7 0.2 - - - -
33K LYS 3.8 0.4 - - - -
34K GLU* 1.3 66.8 - - - +
36K ILE* 1.3 61.5 + - - +
37K PRO* 3.3 5.5 - - - +
920N ALA 3.0 19.6 - - - +
921N ILE* 3.9 6.1 - - - -
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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