Contacts of the strand formed by residues 141 - 145 (chain B) in PDB entry 6W01
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 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B THR* 4.0 5.5 - - - +
122B VAL 3.1 16.4 - - - -
124B PHE* 4.3 5.8 - - - -
135B PHE* 3.7 11.9 - - - -
138B ALA* 5.2 0.4 - - - -
140B ASN* 1.3 76.6 - - - +
142B VAL* 1.3 65.2 + - - +
181B LYS* 3.3 3.6 - - - +
182B LYS* 2.8 36.3 + - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 5.2 0.9 - - + -
76B LEU* 4.0 38.4 - - + +
78B VAL* 3.8 30.1 - - + -
121B THR* 3.9 8.5 - - + -
122B VAL 2.9 6.5 + - - +
123B PHE* 3.4 13.1 - - + -
124B PHE* 2.7 33.3 + - - +
135B PHE* 4.0 2.2 - - - -
141B GLY* 1.3 78.4 - - - +
143B LEU* 1.3 62.9 + - - +
179B TYR* 4.4 8.5 - - + -
180B TYR 3.3 9.6 - - - +
181B LYS* 4.0 14.6 - - + -
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Residues in contact with LEU 143 (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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124B PHE* 3.4 25.8 - - + +
125B ASP 4.4 0.2 - - - -
126B GLY* 3.7 15.3 - - - +
132B VAL* 4.3 23.1 - - + -
135B PHE* 3.6 37.9 - - + -
142B VAL* 1.3 75.9 - - - +
144B ILE* 1.3 76.5 + - - +
145B THR* 4.0 12.6 - - + -
149B VAL* 4.3 7.6 - - + -
152B LEU* 4.6 2.0 - - + -
179B TYR* 3.5 4.7 - - - -
180B TYR* 2.9 53.4 + - + +
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Residues in contact with ILE 144 (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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68B PRO* 3.8 11.0 - - + -
123B PHE* 3.7 35.9 - - + -
124B PHE 3.1 7.7 + - - +
125B ASP* 4.0 9.4 - - - +
126B GLY 2.7 32.4 + - - -
127B ARG* 4.0 20.0 - - - +
142B VAL* 5.1 0.4 - - + -
143B LEU* 1.3 75.3 - - - +
145B THR* 1.3 62.7 + - - +
177B PHE* 3.8 31.0 - - + -
178B ASN 3.2 7.0 - - - +
179B TYR* 3.6 38.8 - - + -
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Residues in contact with THR 145 (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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126B GLY* 4.1 11.2 - - - +
127B ARG* 5.2 2.2 - - - +
132B VAL* 4.2 1.1 - - + -
143B LEU* 4.0 15.3 - - + -
144B ILE* 1.3 79.9 - - - +
146B GLU* 1.3 63.8 + - - +
147B GLY 2.7 25.1 + - - -
149B VAL* 3.6 24.2 - - + -
177B PHE* 3.4 10.9 - - - -
178B ASN* 3.0 40.4 + - - +
180B TYR* 3.5 4.5 - - + -
413B EDO 3.7 17.9 - - - -
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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