Contacts of the strand formed by residues 94 - 99 (chain A) in PDB entry 1W3U
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 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.9 1.8 - - - -
92A GLY 4.9 1.7 + - - -
93A GLN* 1.3 76.7 + - - +
95A ALA* 1.3 57.7 + - - +
96A ASN* 3.2 16.0 + - - +
116A ASP* 3.3 15.9 + - + +
117A THR 3.4 32.5 - - - +
118A HIS* 3.5 17.0 - - + +
140A GLN* 5.7 2.7 + - - -
142A ASN* 2.9 14.3 + - - +
143A ALA* 3.4 2.2 - - - -
144A ALA 2.8 21.4 + - - -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.5 16.1 - - + +
94A THR* 1.3 69.2 - - - +
96A ASN* 1.3 62.6 + - - +
97A TYR* 3.5 12.4 - - + -
111A ALA* 4.5 0.7 - - + -
116A ASP 2.8 15.3 + - - +
117A THR* 3.1 8.2 - - + -
118A HIS 2.8 22.5 + - - +
144A ALA* 4.5 0.9 - - - -
145A TYR* 3.3 41.1 - - + +
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Residues in contact with ASN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 3.2 20.4 - - - +
95A ALA* 1.3 73.8 - - - +
97A TYR* 1.3 59.1 + - - +
118A HIS* 3.1 36.4 + - - +
120A ALA* 3.6 3.7 - - + +
139A LEU* 3.6 27.3 - - + +
140A GLN* 5.4 3.5 + - - +
143A ALA* 3.5 16.0 - - - +
145A TYR* 3.0 17.0 + - - +
146A LEU* 3.3 18.0 - - + -
147A HIS* 2.7 31.9 + - - +
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PHE* 4.7 1.2 + - - -
85A PRO* 4.4 6.4 - - - +
95A ALA* 3.5 30.5 - - + -
96A ASN* 1.3 78.2 - - - +
98A VAL* 1.3 64.6 + - - +
99A MET* 3.6 19.5 + - - +
104A ALA* 4.7 3.1 - - - -
107A ALA* 3.8 21.8 + - + +
108A LEU* 3.8 27.6 - - + -
111A ALA* 3.2 24.3 - - + +
118A HIS 2.8 12.0 + - - +
119A VAL* 3.6 4.9 - - - -
120A ALA 2.9 23.4 + - - -
121A ALA 3.7 2.6 + - - +
145A TYR* 2.8 27.5 + + - -
146A LEU* 4.5 1.3 - - - -
147A HIS* 3.3 39.6 - + + -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TYR* 1.3 73.6 - - - +
99A MET* 1.3 61.3 + - - +
100A THR* 3.5 14.5 + - + -
104A ALA* 3.4 16.3 - - - +
121A ALA* 3.5 7.0 - - + +
132A PRO* 3.9 27.4 - - + -
134A LEU* 3.9 16.8 - - + -
137A ILE* 4.0 17.0 - - + -
146A LEU* 3.7 25.8 - - + -
147A HIS* 2.9 18.7 + - - +
148A LEU* 3.9 19.4 - - + -
149A THR* 4.9 0.2 + - - -
159A PHE* 4.0 8.1 - - + -
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Residues in contact with MET 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TYR* 3.6 26.9 - - - +
98A VAL* 1.3 72.0 - - - +
100A THR* 1.3 61.5 + - - +
101A GLY 3.7 2.2 - - - +
104A ALA* 3.7 6.7 - - - +
105A SER* 3.6 41.1 - - - +
108A LEU* 3.7 26.0 - - + -
119A VAL* 3.5 31.0 - - + -
121A ALA 2.8 13.1 + - - +
122A SER* 3.2 11.8 + - - +
123A SER* 2.9 26.7 + - - -
128A TYR* 4.0 9.0 - - + +
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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