Contacts of the helix formed by residues 12 - 24 (chain v) in PDB entry 4B2Q
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 PHE 12 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26a ASN* 4.9 10.2 - - - +
8v VAL 4.8 3.0 + - - -
9v GLN* 3.2 25.4 + - + +
10v LYS 3.6 9.7 - - - -
13v VAL* 1.3 90.5 + - + +
14v ASP* 3.3 4.3 - - - +
15v LYS* 3.3 19.2 + - - +
16v ILE* 3.1 51.7 + - + +
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Residues in contact with VAL 13 (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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9v GLN 4.8 0.2 - - - +
10v LYS* 3.4 27.6 - - + +
12v PHE* 1.3 93.8 - - + +
14v ASP* 1.3 68.5 + - - +
16v ILE* 3.0 25.6 + - + +
17v ARG* 3.1 57.2 + - - +
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Residues in contact with ASP 14 (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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181t VAL* 6.1 0.2 - - - +
191t LYS* 4.0 26.2 + - - +
194t ILE* 5.1 6.8 - - - +
10v LYS 2.8 25.2 - - - +
12v PHE 3.3 2.4 - - - +
13v VAL* 1.3 82.9 - - - +
15v LYS* 1.3 66.5 + - + +
17v ARG* 3.7 8.4 + - - +
18v GLU* 3.6 23.9 + - - +
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Residues in contact with LYS 15 (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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26a ASN* 6.3 2.2 - - - -
30a THR* 4.4 17.7 - - - +
89a LEU* 4.0 24.5 - - - +
91a LYS* 5.7 7.7 - - - +
177t VAL* 5.0 20.7 - - + +
181t VAL* 5.4 15.6 - - + +
12v PHE* 3.5 20.0 - - - +
13v VAL 3.2 0.4 - - - -
14v ASP* 1.3 77.8 - - + +
16v ILE* 1.3 66.7 + - - +
18v GLU* 3.0 8.3 + - - +
19v TYR* 2.9 20.4 + - - +
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Residues in contact with ILE 16 (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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12v PHE* 3.1 51.1 - - + +
13v VAL* 3.0 18.4 + - + +
15v LYS* 1.3 76.9 - - + +
17v ARG* 1.3 57.9 + - + +
19v TYR* 2.8 21.0 + - + +
20v ARG* 2.7 56.2 + - + +
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Residues in contact with ARG 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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13v VAL* 3.1 42.6 + - - +
14v ASP* 3.9 8.0 + - - +
15v LYS 3.2 0.2 - - - -
16v ILE* 1.3 79.8 - - - +
18v GLU* 1.3 67.5 + - - +
20v ARG* 2.9 47.9 - - - +
21v THR* 3.0 26.2 + - - +
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Residues in contact with GLU 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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176t TRP* 4.9 0.9 - - - -
177t VAL* 5.5 11.7 - - + -
180t ARG* 2.3 64.6 + - + +
181t VAL* 5.0 17.3 - - + -
184t SER* 5.8 4.5 - - - -
188t GLN* 5.9 1.0 + - - -
14v ASP 3.6 12.3 + - - +
15v LYS* 3.0 8.9 + - - +
17v ARG* 1.3 79.6 - - - +
19v TYR* 1.3 68.6 + - - +
21v THR* 3.3 15.2 - - - +
22v LYS* 3.4 9.9 + - - +
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Residues in contact with TYR 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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173t MET* 5.5 13.7 - - + -
177t VAL* 5.9 7.7 - - + +
15v LYS 2.9 11.2 + - - +
16v ILE* 2.8 22.8 + - + +
18v GLU* 1.3 79.0 - - - +
20v ARG* 1.3 65.5 + - + +
22v LYS* 3.2 7.8 + - + +
23v ARG* 2.9 69.6 + - + +
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Residues in contact with ARG 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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16v ILE* 2.7 31.1 + - + +
17v ARG* 2.9 65.0 + - - +
19v TYR* 1.3 76.7 - - + +
21v THR* 1.3 55.3 + - - +
23v ARG* 2.9 35.2 - - - +
24v GLN* 2.9 41.1 + - - +
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Residues in contact with THR 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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176t TRP* 4.7 0.7 - - - -
180t ARG* 2.6 51.4 + - - +
17v ARG 3.0 10.0 + - - +
18v GLU* 3.3 17.3 - - - +
20v ARG* 1.3 75.0 - - - +
22v LYS* 1.3 53.7 + - - +
24v GLN* 3.4 19.1 + - - +
25v THR* 2.7 28.1 + - - -
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Residues in contact with LYS 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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169t GLU 5.1 1.4 + - - -
172t HIS* 5.0 4.9 + - - +
173t MET* 3.0 57.5 - - + +
176t TRP* 2.6 54.7 - - + -
18v GLU 3.4 9.3 + - - +
19v TYR* 3.2 11.8 + - + +
21v THR* 1.3 78.7 - - - +
23v ARG* 1.3 61.1 + - + +
25v THR* 2.8 28.5 + - - +
29v PRO* 4.4 5.5 - - - +
30v VAL* 3.3 44.4 + - + +
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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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173t MET* 5.8 5.2 - - + -
19v TYR* 2.9 50.5 + - + +
20v ARG* 2.9 51.6 + - - +
22v LYS* 1.3 81.0 - - + +
24v GLN* 1.3 72.0 + - - +
25v THR 2.9 9.9 + - - +
26v SER* 5.1 1.9 + - - -
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Residues in contact with GLN 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 ARG* 2.9 36.9 + - - +
21v THR* 3.6 12.9 - - - +
22v LYS 3.1 0.6 - - - -
23v ARG* 1.3 91.3 - - - +
25v THR* 1.3 61.1 + - - +
26v SER* 4.0 4.3 + - - -
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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