Contacts of the strand formed by residues 11 - 16 (chain M) in PDB entry 3Q2K
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 ILE 11 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6M ILE* 3.2 50.5 - - + +
9M ARG 4.7 0.2 - - - +
10M LYS* 1.3 68.9 - - - +
12M ARG* 1.3 67.8 + - - +
13M PHE* 3.7 31.3 + - + -
35M ARG 2.3 28.2 + - - +
36M ALA* 3.3 5.5 - - + +
37M GLU* 2.7 34.4 + - - +
74M ASP* 4.5 6.5 - - + +
75M ALA* 5.2 0.2 - - + -
309M ILE* 4.6 16.2 - - + -
312M LEU* 3.9 30.7 - - + -
313M ARG* 4.7 4.7 - - + +
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Residues in contact with ARG 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M ARG* 3.5 37.8 - - - +
10M LYS 4.3 2.9 - - - +
11M ILE* 1.3 76.9 - - - +
13M PHE* 1.3 62.1 + - - +
37M GLU* 3.9 12.3 - - - +
39M VAL* 3.8 26.7 - - + -
72M ASN* 3.2 41.9 + - - +
73M ALA* 3.6 5.6 - - - -
74M ASP* 2.8 57.2 + - - +
75M ALA 3.4 7.3 + - - -
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Residues in contact with PHE 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M ILE* 3.8 17.5 - - + -
12M ARG* 1.3 72.4 - - - +
14M GLY* 1.3 60.2 + - - +
29M ILE* 4.0 24.5 - - + -
36M ALA* 3.9 29.6 - - + -
37M GLU 3.0 12.9 + - - +
38M LEU* 2.9 27.0 - - + +
39M VAL* 3.0 16.7 + - - +
40M GLU 3.5 1.2 + - - -
73M ALA* 3.9 3.1 - - - -
75M ALA* 3.6 33.0 - - + -
77M VAL* 3.9 13.7 - - + -
100M VAL* 4.5 2.5 - - + -
305M TYR* 3.9 31.0 - + - -
308M VAL* 4.1 17.5 - - + -
309M ILE* 4.3 8.7 - - + -
312M LEU* 4.3 4.0 - - + -
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Residues in contact with GLY 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M PHE* 1.3 74.4 - - - +
15M LEU* 1.3 60.1 + - - -
38M LEU* 3.8 1.8 - - - -
40M GLU* 3.5 15.3 - - - -
67M MET* 5.0 2.0 - - - -
73M ALA* 3.5 9.2 - - - +
75M ALA 3.1 9.5 + - - -
76M LEU* 3.4 18.0 - - - -
77M VAL* 2.7 32.5 + - - +
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Residues in contact with LEU 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M GLY* 1.3 73.8 - - - -
16M VAL* 1.3 64.3 + - - +
17M GLY 2.7 34.5 - - - +
18M CYS* 3.8 13.5 - - - -
22M SER* 3.6 29.2 - - - +
25M HIS* 4.6 8.1 - - + -
26M ILE* 3.7 26.9 - - + -
29M ILE* 5.9 2.0 - - + -
38M LEU* 3.6 15.8 - - + +
40M GLU 3.0 10.0 + - - +
41M ILE* 3.5 4.7 - - + -
42M CYS* 3.0 27.9 + - - +
67M MET* 4.3 1.5 - - - +
77M VAL* 3.8 12.3 - - + +
79M ALA* 4.9 4.7 - - + -
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Residues in contact with VAL 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M LEU* 1.3 73.0 - - - +
17M GLY* 1.3 58.6 + - - +
42M CYS* 3.9 9.9 - - - -
64M LEU* 3.9 15.9 - - + -
67M MET* 3.2 30.7 - - + -
76M LEU* 4.7 6.7 - - + -
77M VAL 2.7 17.2 + - - +
78M LEU* 4.0 16.2 - - + -
79M ALA* 2.7 34.3 + - - +
80M THR* 3.5 10.1 + - + -
88M GLN* 4.0 15.0 - - - +
500M NAI 3.8 22.2 - - + +
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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