Contacts of the strand formed by residues 137 - 142 (chain B) in PDB entry 1W4Z
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 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ASP* 3.1 16.2 - - - -
131B MET* 4.1 9.9 - - - -
134B ARG* 4.3 0.2 - - - -
136B THR* 1.3 77.8 - - - +
138B ARG* 1.3 77.8 + - - +
179B GLY 3.7 4.6 + - - -
180B ILE* 3.3 5.3 - - - +
181B THR 2.9 24.4 + - - -
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Residues in contact with ARG 138 (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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85B ASP 2.8 6.1 + - - +
86B VAL* 3.3 20.0 - - + +
87B LEU 2.8 26.7 + - - -
131B MET* 3.8 1.8 - - - +
136B THR* 6.2 0.2 - - - -
137B GLY* 1.3 86.7 + - - +
139B ILE* 1.3 65.4 + - - +
140B VAL* 4.1 2.9 - - + -
179B GLY 3.8 13.5 + - - -
181B THR* 3.1 28.7 - - - +
239B LEU 3.1 18.4 + - - -
240B ILE* 3.6 35.1 + - + +
241B GLY 2.9 23.2 + - - -
242B PRO* 3.7 10.1 - - - +
245B ALA* 3.7 27.5 - - - +
1267B FMT 5.5 0.6 + - - -
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Residues in contact with ILE 139 (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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87B LEU* 3.4 12.6 - - + +
89B ASN* 4.3 4.5 - - - +
122B THR* 4.0 33.7 - - + +
125B VAL* 5.8 0.7 - - + -
126B LEU* 4.2 10.1 - - + -
131B MET* 3.8 26.9 - - + -
138B ARG* 1.3 79.9 - - - +
140B VAL* 1.3 64.8 + - - +
141B ASN* 4.0 18.4 - - - +
167B PHE* 5.9 0.2 - - + -
171B LEU* 4.4 2.9 - - + -
175B LEU* 4.6 0.2 - - + -
180B ILE* 4.2 6.5 - - + -
181B THR* 3.0 12.4 + - - +
182B VAL* 3.4 33.1 - - + -
183B ASN 2.9 26.0 + - - -
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Residues in contact with VAL 140 (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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86B VAL* 5.7 0.2 - - + -
87B LEU 2.9 10.3 + - - +
88B VAL* 3.4 12.7 - - + +
89B ASN 2.9 25.1 + - - -
138B ARG* 4.8 2.2 - - + -
139B ILE* 1.3 81.7 - - - +
141B ASN* 1.3 64.5 + - - +
142B ILE* 4.5 6.7 - - + -
181B THR* 6.2 1.3 - - + -
183B ASN* 3.2 8.7 - - + +
185B VAL* 3.8 28.0 - - + -
236B VAL* 4.2 16.8 - - + -
239B LEU* 4.3 20.6 - - + -
240B ILE* 3.9 28.0 - - + -
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Residues in contact with ASN 141 (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 ASN* 2.8 38.0 + - + +
118B VAL* 3.6 15.5 - - + +
139B ILE* 4.0 12.8 - - - +
140B VAL* 1.3 76.0 - - - +
142B ILE* 1.3 63.2 + - - +
164B VAL* 3.7 20.4 - - + +
167B PHE* 4.3 9.3 - - - -
168B THR* 3.0 24.7 + - - +
182B VAL* 4.3 4.8 - - - +
183B ASN 2.7 14.9 + - - +
184B ALA* 3.0 7.7 - - + +
185B VAL 2.8 25.1 + - - -
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Residues in contact with ILE 142 (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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18B ILE* 4.6 5.2 - - + -
22B ILE* 3.9 22.4 - - + -
88B VAL* 4.2 9.2 - - + -
89B ASN 3.0 21.8 + - - +
90B ASN* 3.7 26.9 - - + +
118B VAL* 5.9 2.1 - - - +
140B VAL* 4.5 2.7 - - + -
141B ASN* 1.3 73.7 - - - +
143B ALA* 1.3 58.9 + - - +
161B LYS* 2.9 17.2 + - - +
164B VAL* 4.6 5.1 - - - +
185B VAL* 3.6 18.2 - - + -
187B PRO* 3.9 20.6 - - + -
232B VAL* 4.6 3.6 - - + -
236B VAL* 4.3 9.0 - - + -
1262B NAP 3.6 26.7 + - - +
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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