Contacts of the helix formed by residues 3 - 17 (chain B) in PDB entry 5D0A
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 VAL 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ASN* 1.3 89.7 - - - +
4B TYR* 1.3 62.3 + - - +
6B LEU* 3.3 8.1 + - + +
7B LYS* 2.9 27.6 + - + +
176B ILE* 4.3 6.5 - - + -
177B PRO* 3.6 45.8 - - + +
178B PHE* 3.7 24.7 - - + -
179B GLU* 4.6 3.6 - - + +
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Residues in contact with TYR 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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2B ASN 3.3 4.8 - - - +
3B VAL* 1.3 81.1 - - - +
5B GLN* 1.3 64.6 + - + +
7B LYS* 3.4 14.6 + - + +
8B GLU* 3.2 54.9 + - + +
179B GLU* 6.2 2.9 - - + -
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Residues in contact with GLN 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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2B ASN* 3.4 27.2 + - - +
3B VAL 3.2 0.4 - - - -
4B TYR* 1.3 81.7 - - + +
6B LEU* 1.3 65.4 + - - +
8B GLU* 3.3 6.5 + - - +
9B GLU* 3.0 48.4 + - + +
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Residues in contact with LEU 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 ASN 3.0 17.9 + - - +
3B VAL* 3.3 7.8 + - + +
5B GLN* 1.3 73.9 - - - +
7B LYS* 1.3 61.3 - - - +
9B GLU* 3.2 9.2 + - - +
10B LEU* 2.8 31.7 + - - +
119B PHE* 4.0 13.5 - - + -
120B LEU* 4.0 31.0 - - + -
123B LYS* 4.0 23.3 - - + -
124B HIS* 4.7 13.5 - - + -
127B ILE* 4.4 10.3 - - + -
176B ILE* 4.0 23.1 - - + -
178B PHE* 4.0 9.6 - - + -
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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 VAL* 2.9 17.7 + - + +
4B TYR* 3.6 17.7 - - + +
6B LEU* 1.3 77.1 - - - +
8B GLU* 1.3 63.7 + - - +
10B LEU* 3.3 4.3 + - - +
11B ILE* 3.0 45.4 + - + +
24B PHE* 3.6 34.1 - - + -
178B PHE* 3.7 20.8 - - + -
179B GLU* 2.6 45.0 + - + +
180B PRO 4.6 0.2 + - - -
181B ASP* 3.4 17.3 + - - -
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Residues in contact with GLU 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 TYR* 3.2 52.7 + - + +
5B GLN* 3.8 5.8 - - - +
6B LEU 3.3 0.2 - - - -
7B LYS* 1.3 84.6 - - - +
9B GLU* 1.3 59.7 + - + +
11B ILE* 3.8 26.0 - - - +
12B GLU* 3.0 30.4 + - - +
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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 GLN* 3.0 52.3 + - + +
6B LEU* 3.2 10.6 + - - +
8B GLU* 1.3 74.3 - - + +
10B LEU* 1.3 60.3 + - - +
12B GLU* 3.4 12.4 + - - +
13B TYR* 2.9 29.6 + - - +
119B PHE* 3.7 13.4 - - + -
123B LYS* 3.2 31.0 + - - -
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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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6B LEU 2.8 16.8 + - - +
7B LYS 3.6 3.6 - - - +
9B GLU* 1.3 73.8 - - - +
11B ILE* 1.3 54.3 + - - +
13B TYR* 3.1 2.7 + - - +
14B ALA* 2.7 37.0 + - - +
22B ILE* 4.3 7.4 - - + -
24B PHE* 3.8 28.7 - - + -
71B VAL* 4.1 17.5 - - + -
116B LEU* 4.0 32.5 - - + -
119B PHE* 3.9 26.9 - - + -
120B LEU* 4.4 15.0 - - + -
172B MET* 5.1 1.3 - - + -
178B PHE* 4.0 16.6 - - + -
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Residues in contact with ILE 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* 3.0 29.7 + - + +
8B GLU* 3.8 29.8 - - - +
10B LEU* 1.3 76.1 - - - +
12B GLU* 1.3 64.2 + - - +
14B ALA* 3.3 2.8 + - - +
15B LYS* 3.1 50.3 + - + +
22B ILE* 4.0 17.7 - - + -
24B PHE* 3.7 30.3 - - + -
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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 GLU 3.0 19.2 + - - +
9B GLU* 3.6 11.1 - - - +
10B LEU 3.3 0.2 - - - -
11B ILE* 1.3 78.4 - - - +
13B TYR* 1.3 63.9 + - - +
15B LYS* 3.5 5.9 + - - +
16B SER* 3.2 21.5 + - - -
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Residues in contact with TYR 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 16.8 + - - +
10B LEU 3.6 3.1 - - - +
12B GLU* 1.3 75.5 - - - +
14B ALA* 1.3 66.3 + - - +
16B SER* 2.8 30.5 + - - -
17B ILE* 3.1 28.6 + - + +
115B LEU* 3.8 37.8 + - + +
116B LEU* 3.9 14.6 - - + -
119B PHE* 3.4 50.3 - + + -
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Residues in contact with ALA 14 (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 2.7 21.0 + - - +
11B ILE* 3.3 5.1 + - - +
13B TYR* 1.3 73.0 - - - +
15B LYS* 1.3 64.8 + - - +
17B ILE* 3.0 19.5 - - - +
19B VAL* 3.0 36.3 + - + +
22B ILE* 3.7 27.8 - - + -
116B LEU* 3.9 14.3 - - + +
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Residues in contact with LYS 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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11B ILE* 3.1 38.7 + - + +
12B GLU* 4.0 6.1 - - - +
14B ALA* 1.3 79.5 - - + +
16B SER* 1.3 62.9 + - - +
18B GLY* 3.1 12.6 + - - -
19B VAL* 3.6 17.5 - - + +
20B ASP 4.0 18.8 + - - +
21B LYS* 4.7 7.3 - - - +
22B ILE* 4.7 9.6 - - + +
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Residues in contact with SER 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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12B GLU* 3.2 15.1 + - - -
13B TYR* 2.8 31.8 + - - -
15B LYS* 1.3 77.4 - - - +
17B ILE* 1.3 62.0 + - - +
18B GLY* 3.2 0.9 + - - -
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TYR* 3.5 35.2 - - + +
14B ALA* 3.0 17.0 - - - +
16B SER* 1.3 84.5 + - - +
18B GLY* 1.3 56.4 + - - +
19B VAL* 4.4 4.5 - - + -
112B LYS* 2.5 58.3 + - + +
115B LEU* 3.9 32.1 - - + -
116B LEU* 3.9 26.5 - - + -
505B PO4 4.0 1.4 + - - -
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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