Contacts of the strand formed by residues 2 - 11 (chain B) in PDB entry 2HVY
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 LYS 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 71.9 - - - +
3B ARG* 1.3 67.5 + - - +
4B LEU 3.4 0.2 + - - -
22B TRP* 3.4 66.4 - - + +
71B TYR* 3.5 2.0 - - - -
72B VAL* 2.9 38.4 + - - +
74B GLU* 4.5 13.6 - - + +
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Residues in contact with ARG 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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1B MET 4.0 1.2 + - - -
2B LYS* 1.3 74.1 - - - +
4B LEU* 1.3 65.8 + - - +
5B GLY* 4.2 6.3 - - - +
21B ASN* 4.9 5.6 - - - +
22B TRP* 3.0 20.7 + - - -
69B VAL* 3.8 25.8 - - + -
71B TYR* 3.5 35.1 - - + -
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Residues in contact with LEU 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 LYS 3.4 2.8 + - - -
3B ARG* 1.3 76.4 + - - +
5B GLY* 1.3 59.7 + - - +
18B VAL* 3.8 16.2 - - + -
19B ARG 3.5 0.2 - - - +
20B THR* 2.9 35.4 + - - +
21B ASN* 4.6 1.4 + - - +
22B TRP* 3.5 33.9 - - + +
24B PRO* 3.7 16.2 - - + -
30B VAL* 4.3 15.0 - - + -
41B VAL* 4.9 0.7 - - + -
53B VAL* 4.8 6.5 - - + -
55B ILE* 3.9 27.8 - - + -
70B LEU* 3.0 19.6 + - + +
71B TYR 4.5 2.9 - - - +
72B VAL* 3.7 21.5 - - + -
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Residues in contact with GLY 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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3B ARG* 3.9 5.0 - - - +
4B LEU* 1.3 80.4 - - - +
6B LYS* 1.3 65.9 + - - -
7B VAL 3.7 0.5 + - - -
18B VAL* 3.6 11.8 - - - +
19B ARG 3.8 4.7 - - - -
69B VAL* 3.8 14.8 - - - -
70B LEU* 3.0 25.2 + - - -
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Residues in contact with LYS 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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5B GLY* 1.3 74.0 - - - -
7B VAL* 1.3 74.6 + - - +
8B LEU* 3.4 16.4 + - + +
18B VAL* 3.5 16.9 - - - +
19B ARG* 3.9 6.5 + - - +
67B GLY* 3.4 31.2 + - - +
68B GLU 3.7 4.9 - - - -
69B VAL* 4.2 16.1 - - + +
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Residues in contact with VAL 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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6B LYS* 1.3 74.1 - - - +
8B LEU* 1.3 63.5 + - - +
9B HIS 3.6 23.3 - - - +
16B LEU* 3.9 21.1 - - + -
17B ILE 3.6 7.0 - - - +
18B VAL* 3.8 7.9 - - + -
65B TYR* 3.2 29.6 - - + +
66B VAL* 3.9 6.5 - - - -
67B GLY* 2.9 26.5 + - - -
68B GLU 2.9 17.1 + - - +
70B LEU* 3.6 32.1 - - + -
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Residues in contact with LEU 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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127A LYS* 5.7 3.6 - - - +
193A ALA 5.1 0.7 - - - +
6B LYS* 4.2 20.2 - - + +
7B VAL* 1.3 73.9 - - - +
9B HIS* 1.3 83.8 + - + +
17B ILE* 2.8 16.7 + - + +
19B ARG* 4.1 21.8 - - + +
52B TYR* 3.7 33.2 - - + +
66B VAL* 5.0 3.6 - - - +
67B GLY 5.4 0.2 + - - -
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Residues in contact with HIS 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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127A LYS* 4.1 10.8 - - - -
192A LEU 3.5 5.4 + - - -
193A ALA 3.2 28.5 + - - -
194A LEU 3.6 15.3 + - - -
195A GLY* 3.4 23.1 + - - -
7B VAL* 3.4 6.8 - - - +
8B LEU* 1.3 92.8 + - + +
10B TYR* 1.3 63.8 + - - +
11B ALA 3.8 1.3 + - - -
17B ILE* 3.0 45.6 + - + +
66B VAL* 3.9 15.5 - - + -
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Residues in contact with TYR 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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195A GLY 4.7 0.9 - - - +
9B HIS* 1.3 75.5 - - - +
11B ALA* 1.3 71.8 + - - +
12B LYS* 3.5 6.1 + - - -
14B GLY* 3.7 16.2 - - - -
15B PHE 3.6 22.0 - - - -
16B LEU* 3.7 24.7 - - + -
57B PRO* 3.5 25.2 - - + +
62B PRO* 3.5 18.9 - - + +
63B GLU* 3.8 37.5 - - + -
66B VAL* 3.6 13.3 - - + +
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Residues in contact with ALA 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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192A LEU* 4.3 15.9 - - + -
195A GLY* 3.2 24.5 - - - +
9B HIS* 3.8 3.6 + - - -
10B TYR* 1.3 78.7 - - - +
12B LYS* 1.3 56.7 + - - +
13B GLN 3.1 3.6 - - - +
14B GLY* 2.8 23.7 + - - -
15B PHE 2.7 27.5 + - - +
17B ILE* 3.4 19.5 - - + -
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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