Contacts of the strand formed by residues 134 - 140 (chain A) in PDB entry 2W7W
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ALA* 3.5 42.0 - - + +
97A ILE* 4.0 15.9 - - + +
100A ALA* 3.7 23.7 - - + +
101A PHE* 3.9 14.0 - - + -
126A LEU* 3.8 17.0 - - + -
127A VAL 3.4 8.1 - - - +
128A LYS* 4.2 9.0 - - + -
129A ASN* 4.5 0.5 - - - +
132A GLY 3.9 9.4 + - - +
133A SER* 1.3 84.1 - - - +
135A ALA* 1.3 63.3 + - - +
154A LEU* 4.2 17.0 - - + -
192A LEU* 4.3 9.4 - - + -
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Residues in contact with ALA 135 (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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101A PHE* 4.4 4.3 - - - -
125A TRP 3.7 0.2 - - - +
126A LEU* 3.4 6.5 - - - +
127A VAL* 2.9 42.7 + - + +
129A ASN* 3.7 19.1 - - - +
134A LEU* 1.3 77.6 - - - +
136A ILE* 1.3 64.8 + - - +
137A VAL* 4.0 9.2 - - + -
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Residues in contact with ILE 136 (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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101A PHE* 3.8 28.6 - - + -
107A PHE* 4.1 13.2 - - + -
110A LYS* 3.9 13.0 - - + -
111A PHE* 3.5 38.4 - - + +
114A SER* 3.7 29.8 - - - +
124A THR* 3.9 11.4 - - + -
125A TRP 3.2 10.3 - - - +
126A LEU* 4.8 0.7 - - + -
135A ALA* 1.3 75.9 - - - +
137A VAL* 1.3 66.9 + - - +
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Residues in contact with VAL 137 (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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114A SER* 5.1 0.4 - - - -
124A THR* 3.7 0.2 - - - -
125A TRP* 2.7 63.1 + - + -
127A VAL* 3.9 26.9 - - + -
129A ASN* 6.1 0.4 - - - +
135A ALA* 4.0 7.2 + - + -
136A ILE* 1.3 79.3 - - - +
138A ASN* 1.3 65.9 + - - +
139A THR* 4.9 4.3 - - + -
145A PRO* 4.5 9.0 - - + -
148A ASP* 6.0 0.7 - - - +
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Residues in contact with ASN 138 (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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114A SER* 2.6 44.8 + - - +
117A ASN 5.1 1.0 - - - -
118A ASN* 3.3 31.9 + - - +
123A TRP 3.4 4.0 - - - -
124A THR* 2.8 17.4 + - - +
137A VAL* 1.3 75.4 - - - +
139A THR* 1.3 65.6 + - - +
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Residues in contact with THR 139 (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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118A ASN* 3.9 2.9 + - - -
122A SER* 3.2 7.3 - - - -
123A TRP* 2.8 38.5 + - - +
125A TRP* 2.9 30.0 + - + +
137A VAL* 4.9 4.9 - - + -
138A ASN* 1.3 79.3 - - - +
140A SER* 1.3 60.8 + - - +
143A ALA* 2.8 38.8 + - + +
144A THR* 4.0 8.7 - - - +
145A PRO* 4.2 4.9 - - + -
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Residues in contact with SER 140 (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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118A ASN* 5.5 1.3 - - - -
119A PHE 5.1 3.7 + - - -
121A SER 3.8 6.9 + - - -
122A SER* 4.4 2.5 - - - -
139A THR* 1.3 75.9 - - - +
141A ASN* 1.3 83.7 + - - +
142A ALA 3.1 3.5 + - - -
143A ALA* 3.1 19.2 + - - +
141B ASN* 4.5 13.0 + - - -
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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