Contacts of the helix formed by residues 53 - 62 (chain B) in PDB entry 2FHP
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 GLY 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ASP* 4.4 0.2 - - - -
50B SER* 3.0 19.9 + - - -
51B GLY 3.2 2.2 + - - -
52B SER* 1.3 77.8 - - - +
54B GLY* 1.3 65.5 + - - +
55B LEU 3.3 3.4 - - - -
56B ALA* 3.2 5.5 + - - +
57B ILE* 2.9 31.5 + - - +
80B ILE* 3.4 23.6 - - - -
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Residues in contact with GLY 54 (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 MSE 6.1 2.0 - - - -
3B VAL* 6.1 0.2 - - - +
13B LEU* 4.1 25.2 - - - +
29B LYS* 4.0 14.3 + - - +
50B SER 4.6 1.4 + - - -
52B SER* 3.4 12.5 + - - -
53B GLY* 1.3 76.7 - - - +
55B LEU* 1.3 57.6 + - - +
57B ILE* 3.8 2.9 - - - +
58B GLU* 2.9 29.6 + - - +
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Residues in contact with LEU 55 (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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29B LYS* 3.8 30.5 - - + -
32B ILE* 4.7 9.2 - - + -
33B PHE* 3.5 19.7 - - + -
47B ASP* 3.9 12.3 + - - +
50B SER 5.5 1.7 + - - +
53B GLY 3.3 0.8 - - - -
54B GLY* 1.3 72.1 - - - +
56B ALA* 1.3 67.7 + - - +
58B GLU* 3.3 3.2 + - - -
59B ALA* 3.0 19.4 + - - +
118B LEU* 3.9 36.7 - - + +
119B LEU 5.9 0.4 - - - +
120B ASP* 4.7 11.2 - - + +
148B VAL* 5.9 0.4 - - + -
150B GLU* 3.3 26.7 - - - +
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Residues in contact with ALA 56 (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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45B ALA* 5.8 0.2 - - - -
47B ASP* 3.2 25.1 + - + +
50B SER* 4.4 0.2 - - - +
53B GLY 3.2 6.4 + - - +
55B LEU* 1.3 78.2 - - - +
57B ILE* 1.3 63.6 + - + +
59B ALA* 3.2 2.0 + - - +
60B VAL* 3.1 15.9 + - - +
67B SER* 3.1 30.6 + - - -
69B CYS* 3.4 29.4 - - - -
93B PHE* 4.0 4.7 - - + -
118B LEU* 4.4 4.3 - - - -
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Residues in contact with ILE 57 (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* 3.8 28.5 - - + -
8B TYR* 4.0 4.8 - - + -
13B LEU* 4.1 8.7 - - + -
52B SER 4.6 0.2 - - - +
53B GLY* 2.9 26.5 + - - +
54B GLY* 3.9 4.0 - - - +
56B ALA* 1.3 75.2 - - + +
58B GLU* 1.3 59.4 + - - +
60B VAL* 3.4 1.7 + - - +
61B SER* 2.8 28.4 + - - -
80B ILE* 6.3 0.2 - - + -
83B ASN* 3.5 43.7 - - + +
84B ILE* 4.0 7.9 - - + +
87B THR* 3.8 19.3 - - + -
93B PHE* 3.7 24.7 - - + -
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Residues in contact with GLU 58 (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* 3.4 14.8 - - - +
4B ILE* 2.8 30.3 + - - +
5B SER 3.0 21.9 + - - +
29B LYS* 3.8 14.6 + - + -
33B PHE* 3.5 31.2 - - + -
54B GLY 2.9 17.9 + - - +
55B LEU 3.3 5.4 + - - +
57B ILE* 1.3 75.6 - - - +
59B ALA* 1.3 62.6 + - - +
61B SER* 3.4 3.8 + - - -
62B ARG* 2.8 57.9 + - - +
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Residues in contact with ALA 59 (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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33B PHE* 3.7 11.0 - - + -
40B PHE* 3.8 3.1 - - - -
45B ALA* 4.3 2.5 - - + -
55B LEU 3.0 13.4 + - - +
56B ALA* 3.5 9.0 - - - +
57B ILE 3.2 0.6 - - - -
58B GLU* 1.3 77.0 - - - +
60B VAL* 1.3 62.5 + - - +
62B ARG* 3.3 9.2 + - - -
63B GLY 3.3 1.0 + - - -
64B MSE 3.1 31.7 + - - +
67B SER* 4.2 8.3 - - - +
116B LEU* 3.8 29.4 - - + -
118B LEU* 4.8 0.7 - - + -
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Residues in contact with VAL 60 (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 GLU* 5.4 1.7 - - - +
8B TYR* 3.5 23.6 + - - +
56B ALA 3.1 5.1 + - - +
57B ILE 4.0 0.2 - - - +
59B ALA* 1.3 73.8 - - - +
61B SER* 1.3 67.3 + - - +
63B GLY* 2.9 14.6 + - - -
64B MSE 3.6 19.0 - - + +
66B LYS* 4.0 4.7 - - - -
67B SER* 3.3 35.9 - - - +
92B LYS* 3.6 27.3 + - + +
93B PHE* 3.7 28.3 - - + -
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Residues in contact with SER 61 (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* 3.6 11.0 - - - +
5B SER 2.6 25.1 + - - -
6B GLY* 3.2 2.5 - - - -
7B GLU* 2.9 31.1 + - - +
8B TYR* 2.9 43.2 + - - -
57B ILE 2.8 19.3 + - - -
58B GLU 3.5 4.0 - - - -
60B VAL* 1.3 77.7 - - - +
62B ARG* 1.3 56.5 + - - +
63B GLY* 3.4 2.8 + - - -
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Residues in contact with ARG 62 (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 ILE* 3.9 12.1 - - - +
5B SER* 3.4 35.9 + - - +
30B GLU* 4.5 6.5 + - - +
33B PHE* 3.4 37.9 - - - +
34B ASN* 3.2 26.5 + - - -
38B PRO* 2.9 37.8 + - - +
39B TYR* 3.3 25.4 - - + +
40B PHE* 2.8 37.4 + - + +
58B GLU* 2.8 43.4 + - - +
59B ALA 3.3 2.0 + - - -
60B VAL 3.1 0.4 - - - -
61B SER* 1.3 75.4 - - - +
63B GLY* 1.3 56.9 + - - +
64B MSE 3.8 0.2 - - - -
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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