Contacts of the helix formed by residues 2 - 15 (chain B) in PDB entry 4K06
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 LEU 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A VAL* 3.7 32.1 - - + -
33A LEU* 3.7 20.1 - - + +
1B SER* 1.3 74.8 - - - +
3B PHE* 1.3 56.0 + - - +
5B LEU* 3.6 28.1 - - + +
6B GLY 2.8 24.3 + - - -
52B TYR* 5.4 3.8 - - + +
68B PRO 4.3 0.4 + - - +
69B LYS* 3.1 30.4 + - + +
204B 7PE 3.4 46.7 - - - +
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Residues in contact with PHE 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.5 31.4 - - + +
123A LYS* 4.2 5.6 - - + -
125A PRO* 3.6 42.0 - - + -
1B SER* 3.1 12.2 + - - +
2B LEU* 1.3 79.0 - - - +
4B GLU* 1.3 71.9 + - + +
6B GLY* 3.4 0.9 + - - -
7B LYS* 3.0 44.2 + - + +
201B PE4 5.8 1.1 - - - -
204B 7PE 4.2 11.3 - - - +
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Residues in contact with GLU 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B SER* 2.4 48.4 + - - +
3B PHE* 1.3 89.9 - - + +
5B LEU* 1.3 65.7 + - - +
7B LYS* 3.4 4.6 + - - +
8B MET* 3.0 28.9 + - - +
72B ARG* 3.6 14.1 - - - +
73B TYR* 3.4 52.3 + - + +
75B TYR* 3.8 17.4 + - + -
201B PE4 5.8 1.1 - - - -
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Residues in contact with LEU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B SER 3.1 10.0 + - - +
2B LEU* 3.6 28.7 - - + +
3B PHE 3.2 0.2 - - - -
4B GLU* 1.3 76.3 - - - +
6B GLY* 1.3 62.4 + - - +
8B MET* 3.2 2.8 + - - +
9B ILE* 3.0 40.6 + - + +
48B HIS* 3.5 23.8 - - + -
52B TYR* 3.8 6.3 - - - +
73B TYR* 4.0 0.6 + - - -
99B ASP* 3.7 33.9 - - + +
102B VAL* 3.5 31.0 - - + -
204B 7PE 4.1 17.3 - - - +
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Residues in contact with GLY 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU 2.8 12.8 + - - -
5B LEU* 1.3 75.8 - - - +
7B LYS* 1.3 61.4 + - - +
9B ILE* 3.4 1.1 + - - +
10B LEU* 3.0 23.7 + - - +
18B PRO* 3.6 10.4 - - - +
204B 7PE 3.3 45.3 + - - -
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Residues in contact with LYS 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.0 32.7 + - + +
4B GLU* 3.7 3.1 - - - +
6B GLY* 1.3 76.7 - - - +
8B MET* 1.3 58.3 + - - +
10B LEU* 3.3 8.0 + - + +
11B GLN* 2.8 40.8 + - + +
75B TYR* 3.3 16.6 - - + +
201B PE4 2.7 67.0 + - - +
204B 7PE 3.7 21.6 + - - +
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Residues in contact with MET 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLU 3.0 17.0 + - - +
5B LEU 3.5 4.5 - - - +
7B LYS* 1.3 76.4 - - - +
9B ILE* 1.3 54.0 + - - +
11B GLN* 3.1 9.3 + - - +
12B GLU* 2.7 38.3 + - - +
73B TYR* 3.4 34.5 - - + +
75B TYR* 3.6 20.2 - - + +
82B ILE* 3.6 35.7 - - + -
96B CYS* 3.8 14.1 - - - +
99B ASP* 3.5 10.3 - - - +
100B LYS* 3.4 30.5 - - - -
103B ALA* 3.6 8.7 - - + -
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Residues in contact with ILE 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.0 36.5 + - + +
6B GLY 3.7 3.6 - - - +
8B MET* 1.3 74.5 - - - +
10B LEU* 1.3 55.1 + - - +
13B THR* 2.5 43.6 + - + +
18B PRO* 3.7 12.3 - - + -
22B TYR* 3.6 32.5 - - + -
102B VAL* 5.0 2.9 - - + -
103B ALA* 3.9 15.3 - - + +
106B LEU* 3.8 24.2 - - + -
204B 7PE 3.8 37.5 - - - +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 4.8 8.3 - - + -
6B GLY 3.0 13.6 + - - +
7B LYS* 3.5 10.1 - - + +
9B ILE* 1.3 76.9 - - - +
11B GLN* 1.3 60.7 + - + +
15B GLY* 2.6 41.7 + - - +
16B LYS 3.4 31.4 + - - +
17B ASN* 4.1 4.3 - - - +
18B PRO* 4.3 5.6 - - + -
201B PE4 3.5 51.6 - - - +
204B 7PE 3.6 23.6 - - - +
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Residues in contact with GLN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LYS* 2.8 29.8 + - + +
8B MET* 3.5 7.8 - - - +
10B LEU* 1.3 76.0 - - + +
12B GLU* 1.3 62.4 + - - +
15B GLY 4.3 0.5 + - - -
75B TYR* 2.8 30.6 + - - -
77B TRP* 3.6 39.2 - - + +
82B ILE* 4.1 2.0 - - + +
201B PE4 3.1 86.1 + - - +
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B MET 2.7 21.0 + - - +
9B ILE 4.1 0.2 - - - +
11B GLN* 1.3 77.1 - - - +
13B THR* 1.3 62.4 + - - +
77B TRP* 4.2 11.4 - - - -
80B LYS 4.8 3.8 - - - +
81B THR* 5.1 0.7 - - - -
82B ILE* 3.7 32.2 + - + +
103B ALA* 3.3 31.2 - - + +
104B ILE* 3.7 17.4 - - - +
107B ARG* 2.6 61.4 + - + -
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Residues in contact with THR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 2.5 33.3 + - + +
12B GLU* 1.3 74.3 - - - +
15B GLY* 1.3 59.0 + - - +
16B LYS* 3.0 39.7 + - - +
22B TYR* 3.9 13.5 - - + +
103B ALA 3.9 4.7 - - - +
106B LEU* 3.8 16.8 - - + -
107B ARG* 3.6 27.4 - - - +
110B LEU* 3.9 19.7 - - - +
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Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 2.6 33.3 + - - +
12B GLU 3.4 2.0 - - - -
13B THR* 1.3 73.1 - - - +
16B LYS* 1.3 60.7 + - - +
201B PE4 4.4 14.5 - - - +
202B SO4 3.7 10.9 + - - -
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 3.4 17.4 + - - +
13B THR* 3.0 29.6 + - - +
15B GLY* 1.3 82.6 + - - +
17B ASN* 1.3 66.1 + - - +
18B PRO* 3.0 9.7 - - - +
21B SER* 3.5 25.8 - - - +
22B TYR* 4.5 2.0 - - + +
110B LEU* 4.4 24.5 - - + +
118B ARG* 6.0 0.4 - - - +
202B SO4 3.7 21.5 + - - +
203B SO4 5.1 7.9 - - - +
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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