Contacts of the helix formed by residues 84 - 96 (chain B) in PDB entry 4HFG
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 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B VAL* 3.6 33.4 - - + -
42B SER* 6.1 0.9 - - - -
44B TRP* 3.8 23.3 - - + -
45B HIS* 3.7 31.7 + - + +
80B GLU 4.5 2.9 - - - +
81B PHE* 3.1 18.3 + - + +
83B SER* 1.3 83.8 - - - +
85B LEU* 1.3 62.1 + - - +
86B VAL* 3.3 3.7 + - - -
87B ASP* 3.3 8.4 + - - +
88B ALA* 2.9 25.6 + - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 4.4 6.5 - - + -
60B LEU* 4.0 16.4 - - + -
63B ALA* 4.7 2.7 - - + -
67B ILE* 4.1 1.3 - - + -
81B PHE* 3.2 39.2 + - + +
82B GLU 3.8 1.8 + - - -
84B VAL* 1.3 78.3 - - - +
86B VAL* 1.3 56.9 + - - +
88B ALA* 3.7 2.7 - - + -
89B PHE* 2.8 51.0 + - + -
111B TRP* 3.8 27.4 - - + -
117B TYR* 3.8 27.8 - - + +
121B PHE* 4.4 9.9 - - + -
125B LEU* 3.5 14.3 - - + +
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU 4.8 3.0 + - - +
83B SER 5.5 1.1 - - - +
84B VAL 3.3 1.0 - - - -
85B LEU* 1.3 77.5 - - - +
87B ASP* 1.3 62.1 + - - +
90B SER* 3.1 24.5 + - - -
121B PHE* 4.1 16.8 - - + -
124B GLN* 4.5 18.2 - - + +
125B LEU* 3.8 18.6 - - + -
128B SER* 3.6 18.6 + - - -
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B HIS* 2.7 31.2 + - + +
49B ARG* 2.7 36.9 + - - -
84B VAL* 3.3 8.2 + - - +
86B VAL* 1.3 77.0 - - - +
88B ALA* 1.3 57.0 + - - +
90B SER* 4.4 3.9 + - - -
91B HIS* 2.7 34.3 + - - +
94B ARG* 3.9 9.0 + - - -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 3.7 33.4 - - + -
45B HIS* 4.7 2.7 - - + -
48B LEU* 4.0 12.6 - - + -
60B LEU* 4.4 7.4 - - + -
84B VAL 2.9 18.0 + - - +
85B LEU* 3.7 8.7 - - - +
86B VAL 3.3 0.2 - - - -
87B ASP* 1.3 78.7 + - - +
89B PHE* 1.3 57.5 + - - +
91B HIS* 3.3 2.2 + - - +
92B VAL* 2.9 36.2 + - - +
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Residues in contact with PHE 89 (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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60B LEU* 3.8 34.3 - - + -
85B LEU* 2.8 42.9 + - + +
88B ALA* 1.3 70.8 - - - +
90B SER* 1.3 66.5 + - - +
92B VAL* 4.1 0.9 - - - +
93B ALA* 3.0 27.0 + - - +
104B LEU* 3.9 22.6 - - + +
107B LEU* 4.4 9.4 - - + -
108B LEU* 3.5 38.4 - - + -
111B TRP* 4.0 18.6 - + - -
125B LEU* 4.1 14.6 - - + +
128B SER* 3.4 17.5 - - - +
129B MET* 3.9 23.5 - - + +
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 3.1 19.5 + - - -
87B ASP* 3.8 5.8 - - - -
89B PHE* 1.3 76.3 - - - +
91B HIS* 1.3 63.2 + - - +
93B ALA* 3.9 2.2 - - - +
94B ARG* 2.9 55.1 + - - +
128B SER* 3.5 30.1 + - - -
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Residues in contact with HIS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B HIS* 6.5 0.2 - - + -
48B LEU* 4.1 21.3 - - + -
49B ARG* 3.1 53.8 + - + +
56B LYS* 3.1 38.8 + - + -
87B ASP* 2.7 25.2 + - - +
88B ALA* 3.7 3.8 - - - +
90B SER* 1.3 74.4 - - - +
92B VAL* 1.3 57.3 + - - +
94B ARG* 3.8 8.2 + - - +
95B GLU* 2.8 53.9 + - + +
204B UNX 3.7 5.1 - - - -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.8 31.0 - - + -
56B LYS* 4.1 6.3 - - + +
57B LEU* 4.2 17.9 - - + +
60B LEU* 3.6 22.7 - - + -
88B ALA 2.9 20.2 + - - +
89B PHE 4.1 1.3 - - - +
90B SER 3.4 0.2 - - - -
91B HIS* 1.3 75.2 - - + +
93B ALA* 1.3 62.7 + - - +
96B ALA* 2.9 50.3 + - + +
100B CYS* 3.6 5.8 - - - -
104B LEU* 3.9 18.2 - - + -
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Residues in contact with ALA 93 (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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89B PHE 3.0 17.8 + - - +
90B SER 3.9 2.0 - - - +
92B VAL* 1.3 79.9 - - - +
94B ARG* 1.3 60.7 + - + +
96B ALA 4.7 3.3 + - - +
100B CYS* 4.0 15.6 - - - -
101B LYS* 4.9 10.5 - - + +
104B LEU* 4.5 1.7 - - + +
129B MET* 3.7 42.8 - - + +
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Residues in contact with ARG 94 (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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49B ARG* 4.1 6.3 - - - +
87B ASP* 3.9 15.0 + - - -
90B SER* 2.9 40.5 + - - +
91B HIS* 3.8 13.9 - - - +
93B ALA* 1.3 78.6 - - + +
95B GLU* 1.3 85.8 + - + +
96B ALA 3.7 2.5 + - - +
128B SER 5.9 1.1 - - - +
129B MET 5.8 3.1 - - - +
204B UNX 3.4 18.8 - - - -
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER* 3.0 21.7 + - - -
56B LYS* 3.7 21.8 - - - -
91B HIS* 2.8 41.4 + - + +
94B ARG* 1.3 98.2 + - + +
96B ALA* 1.3 60.6 + - - +
204B UNX 4.1 6.1 - - - -
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER* 3.6 14.4 - - - +
56B LYS* 4.0 13.2 - - + +
57B LEU* 4.7 5.2 - - + +
92B VAL* 2.9 37.2 + - + +
93B ALA 4.8 3.1 - - - +
94B ARG 4.7 2.6 - - - +
95B GLU* 1.3 81.7 + - - +
97B ASP* 1.3 72.9 + - - +
98B GLU* 3.5 1.9 + - - -
100B CYS* 4.3 7.5 - - + -
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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