Contacts of the helix formed by residues 16 - 25 (chain V) in PDB entry 3S1K
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 LYS 16 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B LYS* 4.6 13.5 - - - +
7B GLU* 3.2 50.7 + - - +
10B ASN* 3.4 31.0 - - + +
13V GLU* 5.1 10.0 + - - -
14V VAL 3.3 8.2 + - - +
15V VAL* 1.3 74.2 - - - +
17V PHE* 1.3 67.8 + - - +
18V MET* 4.4 3.4 - - + +
19V ASP* 2.9 25.9 + - - +
20V VAL* 2.9 22.3 + - - +
79W GLN* 3.3 10.5 - - - +
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Residues in contact with PHE 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 3.3 4.7 + - - +
13B ALA* 4.2 11.9 - - + -
14B ILE* 4.1 13.5 - - + -
17B ALA* 3.6 30.1 - - + -
27B PHE* 4.1 13.5 - + - -
31B ILE* 4.3 12.1 - - + -
16V LYS* 1.3 71.5 - - - +
18V MET* 1.3 62.0 + - - +
20V VAL* 3.3 1.5 + - - +
21V TYR* 2.8 44.2 + + + +
48W LYS 3.2 27.4 - - - -
49W PRO* 4.1 5.8 - - + -
79W GLN* 2.7 49.4 + - + +
81W MET* 4.1 5.4 - - + -
91W ILE* 4.0 21.5 - - + -
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Residues in contact with MET 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LYS 4.7 5.2 - - - +
9B HIS* 3.8 23.6 - - + +
10B ASN* 3.0 43.7 + - + +
13B ALA* 4.0 13.5 - - + -
31B ILE* 5.4 2.5 - - + -
34B LEU* 4.4 12.6 - - + +
35B ILE* 3.9 39.9 - - + +
38B PRO* 5.2 4.3 - - + -
16V LYS* 4.9 2.0 - - + -
17V PHE* 1.3 82.2 - - - +
19V ASP* 1.3 75.8 + - - +
21V TYR* 3.9 4.0 - - - +
22V GLN* 3.1 28.1 + - - +
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Residues in contact with ASP 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V VAL* 4.2 11.9 - - + -
16V LYS* 2.9 30.8 + - - +
18V MET* 1.3 87.9 - - - +
20V VAL* 1.3 65.0 + - - +
22V GLN* 4.0 12.4 - - - +
23V ARG* 3.0 42.2 + - - +
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Residues in contact with VAL 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V VAL* 3.5 28.9 - - + +
16V LYS 2.9 17.8 + - - +
17V PHE 3.7 3.6 - - - +
19V ASP* 1.3 74.6 - - - +
21V TYR* 1.3 58.2 + - - +
23V ARG* 3.9 3.0 - - - +
24V SER* 2.6 36.6 + - - +
49W PRO* 3.8 18.8 - - + -
52W VAL* 4.0 8.1 - - + -
53W PRO* 4.3 8.9 - - + +
78W MET* 3.9 29.8 - - + -
79W GLN 3.9 10.1 - - - +
80W ILE* 3.9 10.5 - - + -
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Residues in contact with TYR 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 4.1 24.0 - + - -
28B HIS* 3.2 41.9 + + - +
31B ILE* 4.1 22.2 - - + -
32B TRP* 4.1 15.5 - + - -
35B ILE* 4.6 0.7 - - + -
17V PHE* 2.8 31.4 + + + +
18V MET* 3.9 7.2 - - - +
20V VAL* 1.3 79.4 - - - +
22V GLN* 1.3 64.6 + - - +
24V SER* 3.4 5.1 + - - -
25V TYR* 3.2 26.8 + + - +
61V CYS 4.8 0.3 + - - -
62V ASN* 3.3 40.3 + - + +
48W LYS* 4.9 3.5 + - + -
49W PRO* 4.1 19.5 - - + +
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Residues in contact with GLN 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TRP* 3.9 21.4 - - + -
35B ILE* 3.6 34.3 - - + +
18V MET* 3.1 14.6 + - - +
19V ASP* 4.0 15.1 - - - +
20V VAL 3.4 0.2 - - - -
21V TYR* 1.3 81.6 - - - +
23V ARG* 1.3 68.2 + - + +
24V SER 3.4 0.3 + - - -
25V TYR* 3.5 14.0 + - - +
27V HIS* 5.0 1.9 + - - -
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Residues in contact with ARG 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V VAL* 3.8 29.5 - - - +
19V ASP* 3.0 29.7 + - + +
20V VAL 4.2 0.4 - - - +
22V GLN* 1.3 84.4 - - + +
24V SER* 1.3 57.4 + - - +
25V TYR 3.4 0.2 - - - -
27V HIS* 3.2 23.8 + - - -
30W GLU* 3.1 34.9 + - - +
32W LEU* 3.9 8.0 - - - +
53W PRO* 3.7 37.4 + - + +
78W MET* 5.9 0.8 - - - +
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Residues in contact with SER 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V VAL 2.6 21.8 + - - -
21V TYR 3.4 3.8 + - - -
23V ARG* 1.3 77.2 - - - +
25V TYR* 1.3 60.7 + - - +
27V HIS* 4.6 0.2 - - - -
59V GLY* 3.1 10.2 - - - -
60V CYS* 2.9 25.4 + - - -
62V ASN* 5.6 0.2 + - - -
32W LEU* 3.8 11.7 - - - -
49W PRO* 3.2 22.4 - - - +
51W CYS* 3.1 30.1 - - - -
53W PRO* 4.2 6.1 - - - -
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Residues in contact with TYR 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B HIS* 3.1 43.2 + + - -
32B TRP* 3.7 35.9 - + + -
21V TYR* 3.2 21.2 + + - +
22V GLN 3.5 3.1 + - - +
23V ARG 3.4 1.2 - - - -
24V SER* 1.3 78.9 - - - +
26V CYS* 1.3 75.7 + - + +
27V HIS* 2.4 34.1 + - - +
58V GLY 4.3 0.4 - - - -
60V CYS* 3.3 19.1 - - - -
61V CYS 3.9 14.2 + - - -
62V ASN* 4.1 12.8 - - - +
66V LEU* 5.8 0.5 - - - +
104V CYS* 3.2 33.2 - - + +
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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
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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