Contacts of the strand formed by residues 149 - 156 (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 THR 149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASN* 4.1 28.7 + - + +
92B ASN 4.2 10.1 - - - -
93B PRO* 3.4 16.0 - - + +
94B SER* 2.9 35.5 + - - -
95B LEU 3.7 3.1 + - - -
148B MET* 1.3 71.4 - - - +
150B ILE* 1.3 63.5 + - - +
183B THR* 4.4 11.0 - - + -
184B LEU 3.7 5.6 - - - +
185B MET* 3.5 16.8 - - + +
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PRO* 4.5 0.9 - - - -
95B LEU* 3.4 18.2 - - + +
97B VAL* 3.9 20.0 - - + -
144B LEU* 3.8 20.0 - - + -
145B PRO* 3.8 38.4 - - + +
148B MET* 3.7 13.2 - - + +
149B THR* 1.3 79.4 - - - +
151B ARG* 1.3 72.1 + - - +
152B MET* 3.5 12.8 + - + -
183B THR* 3.4 9.1 - - - +
184B LEU* 3.0 49.7 + - + +
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Residues in contact with ARG 151 (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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93B PRO* 3.6 30.8 - - + +
95B LEU 2.9 9.3 + - - +
96B THR* 2.6 49.2 + - - +
97B VAL 2.8 29.1 + - - +
150B ILE* 1.3 73.2 - - - +
152B MET* 1.3 62.7 + - - +
153B LEU* 4.2 11.7 - - - -
181B GLN* 2.8 39.8 + - + +
182B THR 3.8 2.5 - - - -
183B THR* 4.4 5.2 - - + -
13H THR* 3.8 3.4 + - - +
14H ALA* 2.8 35.8 + - - +
15H PRO 3.7 15.6 + - - -
16H PHE* 4.0 6.1 - - - +
25H GLN* 5.6 0.8 + - - -
28H ASN* 6.0 2.7 - - - +
63H LEU* 4.0 12.4 - - - +
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Residues in contact with MET 152 (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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97B VAL* 3.4 39.3 - - + +
99B THR* 3.8 33.0 - - + +
108B TYR* 4.9 2.5 - - + -
142B VAL* 5.6 1.3 - - + -
144B LEU* 4.9 6.7 - - - -
150B ILE* 3.5 7.1 + - + -
151B ARG* 1.3 73.6 - - - +
153B LEU* 1.3 62.3 + - - +
154B VAL* 4.7 3.4 - - + -
163B TRP* 3.9 29.4 - - + -
180B ASN 3.7 0.5 - - - +
181B GLN* 3.4 5.4 - - - +
182B THR* 2.9 50.5 + - + +
184B LEU* 3.9 33.0 - - + -
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR* 3.9 16.2 - - + -
97B VAL 2.9 6.7 + - - -
98B LYS* 3.3 14.8 - - + +
99B THR* 2.8 28.8 + - - +
100B MET* 5.9 0.2 - - - +
151B ARG* 4.2 14.1 - - - -
152B MET* 1.3 73.6 - - - +
154B VAL* 1.3 61.5 + - - +
179B LEU* 4.2 18.4 - - + -
180B ASN 3.4 2.9 - - - +
181B GLN* 4.0 27.1 - - + +
25H GLN* 4.0 19.1 - - + -
63H LEU* 3.2 48.0 - - + +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B THR* 3.6 21.3 - - + -
106B TRP* 4.8 0.9 - - + -
152B MET* 4.7 7.6 - - + +
153B LEU* 1.3 79.6 - - - +
155B SER* 1.3 65.5 + - - +
163B TRP* 4.0 23.6 - - + -
172B THR* 3.8 36.8 - - + +
173B ASP 3.8 2.2 - - - +
174B ALA* 3.6 28.5 - - + -
175B ILE 5.1 0.3 + - - -
178B ARG 3.7 1.0 - - - +
179B LEU* 3.7 1.2 - - - -
180B ASN* 2.7 39.5 + - - +
182B THR* 4.9 1.8 - - + -
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Residues in contact with SER 155 (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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99B THR 3.1 10.9 + - - +
100B MET* 3.7 20.3 - - - +
101B GLY 2.8 19.7 + - - -
154B VAL* 1.3 72.3 - - - +
156B SER* 1.3 74.3 + - - +
174B ALA* 3.3 12.2 - - - +
175B ILE 3.2 11.5 + - - +
177B GLY 4.2 0.3 + - - -
178B ARG 2.7 27.6 + - - -
179B LEU* 4.1 12.1 - - - -
68H TRP* 4.0 10.7 - - - -
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B MET* 3.8 8.5 - - - +
101B GLY 3.6 7.4 + - - +
155B SER* 1.3 82.0 + - - +
157B GLU* 1.3 63.0 + - - +
158B ASP* 2.9 14.4 + - - -
159B VAL 2.6 29.5 + - - -
161B HIS* 3.6 8.5 - - - -
174B ALA* 3.6 15.7 - - - -
175B ILE 3.9 3.6 - - - -
176B PRO* 3.4 26.1 - - - +
177B GLY 4.5 1.0 + - - -
68H TRP* 5.3 2.1 + - - -
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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
------------------------------------------------------------
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