Contacts of the helix formed by residues 4 - 13 (chain B) in PDB entry 2ZHX
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 4 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A SER 6.1 0.9 - - - +
137A PRO* 5.6 2.0 - - + -
3B ASN* 1.3 72.4 - - - +
5B SER* 1.3 55.9 + - - +
6B ASP 3.1 2.9 - - - -
7B ILE* 3.0 31.4 + - + +
8B ILE 3.9 2.8 + - - -
18B ILE* 3.4 26.0 - - + -
44B HIS* 3.9 25.1 - - + +
57B LEU* 3.6 23.1 - - + +
59B THR* 4.7 3.1 - - + -
65B TYR* 3.6 44.4 - - + +
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Residues in contact with SER 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASN* 2.7 31.6 + - - +
4B LEU* 1.3 76.2 - - - +
6B ASP* 1.3 60.8 + - - +
7B ILE 3.3 0.2 - - - -
8B ILE* 3.3 15.0 + - - +
9B GLU* 3.0 24.1 + - - +
14B LYS 5.1 0.9 - - - +
16B LEU 3.7 22.7 + - - +
17B VAL* 5.3 0.9 - - - -
18B ILE* 4.5 23.1 - - - +
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Residues in contact with ASP 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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3B ASN* 3.1 42.8 + - - +
4B LEU 3.1 0.2 - - - -
5B SER* 1.3 80.9 + - - +
7B ILE* 1.3 58.3 + - + +
9B GLU* 2.9 25.5 + - - +
10B LYS* 2.8 26.7 + - - +
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Residues in contact with ILE 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASN 4.7 1.8 - - - +
4B LEU* 3.0 28.3 - - + +
6B ASP* 1.3 72.3 - - + +
8B ILE* 1.3 64.3 + - - +
10B LYS* 3.4 19.6 - - + +
11B GLU* 3.1 30.1 + - + +
57B LEU* 3.6 25.8 - - + -
67B PRO* 3.2 40.8 - - + -
70B LEU* 5.4 0.6 - - + +
84B LEU* 4.4 7.6 - - + -
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Residues in contact with ILE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU 3.9 0.6 + - - -
5B SER* 3.3 15.7 + - - +
6B ASP 3.2 0.6 - - - -
7B ILE* 1.3 73.0 - - - +
9B GLU* 1.3 57.2 + - - +
10B LYS 2.8 9.4 + - - -
11B GLU* 3.0 4.1 + - - -
12B THR* 2.7 39.9 + - + +
14B LYS 4.2 11.4 - - - +
16B LEU* 4.9 13.7 - - + +
18B ILE* 4.1 28.5 - - + -
44B HIS 5.3 1.1 - - - +
46B ALA* 4.7 10.5 - - + -
55B VAL* 4.2 31.4 - - + +
57B LEU* 3.8 31.6 - - + -
70B LEU* 5.3 7.9 - - + -
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Residues in contact with GLU 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 SER 3.0 12.5 + - - +
6B ASP* 2.9 27.3 + - - +
8B ILE* 1.3 75.2 - - - +
10B LYS* 1.3 56.5 + - - +
13B GLY* 2.9 27.1 + - - -
14B LYS 3.9 31.6 - - - +
15B GLN* 5.0 10.2 - - + +
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Residues in contact with LYS 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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6B ASP 2.8 11.4 + - - +
7B ILE* 3.4 21.0 - - - +
8B ILE 2.9 0.2 - - - -
9B GLU* 1.3 80.1 - - - +
11B GLU* 1.3 82.8 - - - +
12B THR 3.2 1.1 + - - -
13B GLY* 4.4 1.2 + - - -
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Residues in contact with GLU 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 ILE* 3.1 15.6 + - - +
8B ILE 3.0 2.6 + - - +
10B LYS* 1.3 104.1 - - - +
12B THR* 1.3 61.5 + - - +
70B LEU* 3.6 27.0 - - + +
82B LYS* 3.2 39.4 + - + +
84B LEU* 3.5 27.5 - - + +
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Residues in contact with THR 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 ILE* 2.7 28.1 + - + +
10B LYS 3.2 0.6 - - - -
11B GLU* 1.3 85.7 - - - +
13B GLY* 1.3 62.7 + - - +
14B LYS* 3.7 18.7 + - - +
55B VAL* 5.1 8.2 - - + +
70B LEU* 4.0 18.6 - - + -
72B ILE* 3.8 29.4 - - + -
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Residues in contact with GLY 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 GLU* 2.9 25.2 + - - -
10B LYS 4.4 1.0 + - - -
12B THR* 1.3 79.1 + - - +
14B LYS* 1.3 68.4 + - - +
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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