Contacts of the strand formed by residues 95 - 102 (chain B) in PDB entry 5W97
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 LEU 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PRO* 3.5 2.5 - - - +
94B SER* 1.3 83.5 - - - +
96B THR* 1.3 65.9 + - - +
97B VAL* 3.9 23.3 - - + -
110B TYR* 4.5 8.3 - - + -
112B ASP* 3.2 24.7 - - + +
113B TYR* 5.2 10.1 - - + +
144B LEU* 4.6 0.7 - - + -
145B PRO* 3.8 20.2 - - + -
148B MET* 4.7 5.8 - - + -
149B THR 3.7 1.4 + - - -
150B ILE* 3.4 16.4 - - + -
151B ARG* 2.9 26.0 + - - +
219B PHE* 3.6 37.2 - - + -
13H THR* 4.1 3.6 - - - -
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Residues in contact with THR 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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95B LEU* 1.3 76.6 - - - +
97B VAL* 1.3 70.3 + - - +
98B LYS* 4.9 1.1 - - + -
109B GLU 4.5 2.9 - - - +
110B TYR* 4.6 5.9 - - - -
111B THR 4.8 2.1 + - - -
112B ASP* 3.0 21.1 + - - +
151B ARG* 2.6 45.1 + - - +
153B LEU* 3.9 24.2 - - + -
13H THR* 2.8 14.5 + - - -
62H SER* 3.5 24.4 - - - +
63H LEU* 4.4 1.8 - - + +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.9 11.7 - - + -
96B THR* 1.3 79.8 - - - +
98B LYS* 1.3 70.8 + - - +
108B TYR* 4.9 6.5 - - + -
109B GLU 3.6 12.6 - - - +
110B TYR* 3.9 36.6 - - + +
142B VAL* 5.1 1.1 - - + -
144B LEU* 3.7 26.0 - - + -
150B ILE* 3.9 7.2 - - + -
151B ARG 2.8 8.1 + - - +
152B MET* 3.4 23.7 - - + +
153B LEU* 2.9 24.1 + - - +
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Residues in contact with LYS 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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96B THR 5.9 0.4 - - - -
97B VAL* 1.3 78.2 - - - +
99B THR* 1.3 63.2 + - - +
100B MET* 5.3 4.0 - - + -
108B TYR* 3.3 4.9 - - - +
109B GLU* 2.8 73.3 + - + +
111B THR* 2.9 37.2 + - - +
152B MET* 4.6 0.2 - - - -
153B LEU* 3.3 27.4 - - + +
179B LEU* 5.4 0.4 - - + -
61H LYS 3.9 0.2 + - - -
62H SER 3.5 12.1 - - - +
63H LEU 3.6 12.1 - - - +
64H CYS 2.8 32.6 + - - +
65H PRO* 3.8 8.5 - - + +
66H ILE* 3.9 2.4 - - - +
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Residues in contact with THR 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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98B LYS* 1.3 74.6 - - - +
100B MET* 1.3 66.3 + - - +
101B GLY 4.1 0.4 - - - -
106B TRP* 3.4 17.2 - - + +
107B SER 3.4 5.7 + - - -
108B TYR* 3.2 30.4 - - - -
152B MET* 3.8 14.1 - - + -
153B LEU 2.8 11.6 + - - +
154B VAL* 3.7 30.5 - - + -
155B SER 3.1 25.3 + - - +
163B TRP* 3.8 16.7 + - + -
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Residues in contact with MET 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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98B LYS* 5.3 3.4 - - + -
99B THR* 1.3 80.5 + - - +
101B GLY* 1.3 60.6 + - - +
102B HIS* 3.0 25.5 - - + +
106B TRP* 3.7 4.2 - - - -
107B SER* 2.9 33.5 + - - +
109B GLU* 3.9 25.1 - - + +
153B LEU 5.9 0.2 - - - +
155B SER* 3.4 24.5 - - - +
156B SER 3.8 17.3 - - - +
157B GLU* 3.5 36.1 - - + +
179B LEU* 5.4 0.2 - - - -
65H PRO* 3.8 28.5 - - + -
67H SER* 4.5 1.6 - - - +
68H TRP* 4.6 5.2 - - - +
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Residues in contact with GLY 101 (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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100B MET* 1.3 72.8 - - - +
102B HIS* 1.3 63.9 + - - -
106B TRP* 3.5 26.2 - - - -
155B SER 2.8 16.6 + - - -
156B SER* 3.6 1.1 + - - +
157B GLU* 3.1 23.4 + - - -
158B ASP* 4.2 0.2 - - - +
161B HIS* 3.6 19.3 - - - -
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Residues in contact with HIS 102 (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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100B MET* 3.0 27.3 + - + +
101B GLY* 1.3 75.9 + - - -
103B GLN* 1.3 59.8 + - - +
104B TRP* 3.0 2.8 - - - -
105B TYR* 2.9 78.1 + + + +
107B SER* 3.0 26.9 + - - -
157B GLU* 3.9 36.3 - - + +
158B ASP* 3.5 9.9 + - - +
161B HIS* 3.2 18.1 + - - -
207B MET* 3.4 2.6 - - - +
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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