Contacts of the helix formed by residues 10 - 18 (chain B) in PDB entry 5H4G
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 ASP 10 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PHE* 1.3 75.7 - - - +
11B SER* 1.3 66.7 + - - +
12B LEU* 3.7 6.5 + - - +
13B ALA* 3.3 21.7 + - - +
14B LEU* 2.9 20.4 + - - +
41B THR* 3.7 4.3 - - - -
97B GLU* 5.2 2.0 - - - +
101B THR* 4.1 15.7 - - + +
112B LEU* 3.7 2.5 - - + +
113B VAL 3.4 4.8 + - - -
114B THR* 2.7 30.5 + - - -
115B ASP 4.5 1.2 + - - -
119B ARG* 3.3 13.4 + - - +
120B TYR* 2.7 28.4 + - + +
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Residues in contact with SER 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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10B ASP* 1.3 77.1 - - - +
12B LEU* 1.3 73.2 + - - +
14B LEU* 3.3 2.8 + - - +
15B ILE* 2.9 36.5 + - - +
41B THR* 3.7 19.9 - - - +
44B ARG* 3.4 25.4 - - - +
45B TYR* 4.4 3.5 - - - +
97B GLU* 2.7 31.1 + - - -
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 3.4 6.9 + - - +
11B SER* 1.3 89.6 - - - +
13B ALA* 1.3 63.3 + - - +
15B ILE* 3.3 15.3 + - + +
16B LYS* 3.1 32.5 + - - +
44B ARG* 6.3 0.9 - - - -
115B ASP* 5.5 11.4 - - + +
119B ARG* 4.7 21.1 - - - +
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Residues in contact with ALA 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 PHE* 4.0 12.1 - - + -
10B ASP* 3.3 20.8 + - - +
12B LEU* 1.3 76.8 - - - +
14B LEU* 1.3 59.8 + - - +
16B LYS* 3.2 4.0 + - - +
17B MET* 2.9 33.8 + - - +
113B VAL 3.7 18.4 - - - +
114B THR* 4.3 6.7 - - - -
115B ASP* 4.7 2.8 - - - +
133B LEU* 4.2 23.2 - - + +
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 3.9 15.4 - - + +
10B ASP 2.9 16.8 + - - +
11B SER* 3.7 5.8 - - - +
13B ALA* 1.3 76.2 - - - +
15B ILE* 1.3 63.5 + - - +
17B MET* 3.1 5.6 + - + +
18B HIS* 3.1 32.0 + - + +
37B LEU* 3.9 28.5 - - + -
41B THR* 4.0 15.5 - - + +
42B VAL* 5.1 2.5 - - + -
45B TYR* 3.8 33.9 - - + -
63B LEU* 5.4 2.9 - - + -
67B TYR* 3.6 31.2 - - + +
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Residues in contact with ILE 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 SER* 2.9 28.3 + - - +
12B LEU* 3.6 16.4 - - + +
13B ALA 3.2 0.2 - - - -
14B LEU* 1.3 75.0 - - - +
16B LYS* 1.3 65.5 + - + +
18B HIS* 3.1 14.7 + - - +
19B SER* 3.5 9.0 + - - -
44B ARG 4.6 3.4 - - - +
45B TYR* 3.6 33.6 - - + -
48B ALA* 3.9 27.6 - - + -
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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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12B LEU* 3.1 18.7 + - - +
13B ALA 3.5 7.0 - - - +
15B ILE* 1.3 78.3 - - + +
17B MET* 1.4 59.4 + - - +
19B SER* 2.6 30.0 + - - -
22B MET* 3.2 12.6 - - + +
115B ASP* 3.0 32.9 + - - +
133B LEU* 3.6 23.8 - - + +
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Residues in contact with MET 17 (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 PHE* 3.6 39.9 - - + -
13B ALA 2.9 19.5 + - - +
14B LEU* 3.1 13.4 + - + +
16B LYS* 1.4 76.7 - - - +
18B HIS* 1.3 63.9 + - + +
19B SER 3.3 1.7 + - - +
22B MET* 3.6 37.1 - - - +
23B LYS* 5.4 0.2 - - - -
25B ILE* 4.0 3.4 - - + -
26B LEU* 3.6 49.8 - - + +
29B THR* 3.6 24.0 - - - +
133B LEU* 4.3 6.5 - - + -
136B PHE* 4.0 11.9 - - + -
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Residues in contact with HIS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.1 27.1 + - + +
15B ILE 3.1 9.7 + - - +
17B MET* 1.3 79.9 - - + +
19B SER* 1.3 64.4 + - - +
20B GLN* 3.9 0.5 + - - +
26B LEU* 4.2 18.0 - - + +
45B TYR* 3.3 26.5 + + + +
49B ARG* 5.9 2.6 + - - +
59B GLU* 4.3 3.7 + - - -
62B ILE* 5.6 3.1 - - + -
63B LEU* 3.8 23.0 - - + +
66B ILE* 4.3 8.7 - - + -
67B TYR* 2.7 35.0 + + - -
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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