Contacts of the strand formed by residues 95 - 100 (chain B) in PDB entry 4B5G
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 PHE 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B HIS* 3.2 6.5 + - - -
69B VAL* 3.5 3.8 - - - +
81B GLN* 4.1 15.0 - - - -
83B GLY* 3.2 46.6 + - - -
84B MET* 3.7 29.8 - - + +
90B ASP* 4.9 0.4 - - - +
93B GLY 3.7 0.2 - - - -
94B ARG* 1.3 81.0 - - - +
96B VAL* 1.3 70.4 + - - +
97B ARG* 3.6 25.4 - - + -
106B ILE* 3.5 44.6 - - + -
107B SER 3.4 4.9 - - - -
108B LEU* 4.4 8.1 - - + -
126B PHE* 6.2 0.2 - - + -
130B PHE* 4.2 26.5 - + - -
133B MET* 6.6 0.2 - - + -
137B MET* 4.3 6.3 - - + -
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Residues in contact with VAL 96 (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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57B HIS* 3.5 24.7 - - + +
58B TRP 3.8 4.0 - - - +
59B HIS* 3.6 30.1 - - + +
69B VAL* 3.6 17.9 - - + +
71B VAL* 4.0 18.7 - - + +
80B VAL* 5.1 2.2 - - + -
81B GLN 3.8 7.4 - - - +
82B ILE* 5.4 3.6 - - + -
95B PHE* 1.3 84.3 - - - +
97B ARG* 1.3 65.1 + - - +
98B CYS* 4.2 12.6 - - - -
105B VAL 4.0 0.2 - - - +
106B ILE* 3.2 6.6 - - - +
107B SER* 2.9 33.0 + - - +
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Residues in contact with ARG 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.3 5.2 - - - +
81B GLN* 2.9 57.5 + - + +
95B PHE* 3.6 18.1 - - + -
96B VAL* 1.3 74.5 - - - +
98B CYS* 1.3 68.9 + - - +
99B ASP* 3.0 20.2 + - - +
104B SER* 2.8 23.6 + - - +
105B VAL 3.6 2.9 - - - -
106B ILE* 3.6 21.5 - - + -
137B MET* 3.9 22.2 - - - +
140B GLU* 2.7 40.4 + - - -
142B ARG* 3.7 8.5 - - - +
144B ILE* 3.4 12.8 - - - +
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Residues in contact with CYS 98 (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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57B HIS* 4.2 22.7 - - - -
71B VAL* 4.0 29.8 - - + -
73B SER* 5.9 0.2 - - - -
77B PRO* 4.0 11.4 - - + -
79B ASN 3.5 3.6 - - - -
80B VAL* 4.2 9.4 - - - -
96B VAL* 4.2 2.7 - - - -
97B ARG* 1.3 81.8 - - - +
99B ASP* 1.3 63.3 + - - +
100B PHE* 3.5 25.7 - - + -
104B SER* 3.4 2.3 - - - -
105B VAL 2.9 37.6 + - - +
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Residues in contact with ASP 99 (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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77B PRO 3.5 1.7 - - - -
78B ASP* 2.8 37.3 + - - +
79B ASN* 2.9 42.0 + - + +
97B ARG* 3.0 20.7 + - - -
98B CYS* 1.3 73.1 - - - +
100B PHE* 1.3 58.7 + - - +
101B GLY 4.8 0.4 - - - +
103B LEU 3.6 2.9 - - - -
104B SER* 2.5 29.5 + - - -
142B ARG* 3.7 18.2 + - - +
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Residues in contact with PHE 100 (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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31B ILE* 4.0 20.6 - - + -
71B VAL* 5.1 2.5 - - + -
73B SER* 3.4 37.0 - - - -
75B ARG* 3.4 44.5 + - + +
76B LYS 4.1 6.1 - - - -
77B PRO* 3.5 29.4 - - + -
78B ASP* 3.4 7.6 - - - +
98B CYS* 3.5 31.0 - - + -
99B ASP* 1.3 71.8 - - - +
101B GLY* 1.3 57.2 + - - +
102B ARG 3.3 5.5 + - - -
103B LEU* 2.9 32.4 + - + +
105B VAL* 4.3 11.0 - - + -
258B ALA 5.7 0.9 - - - +
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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