Contacts of the strand formed by residues 134 - 140 (chain B) in PDB entry 2AWP
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 3.9 15.9 - - + -
96B LYS* 3.5 41.5 - - + +
97B ILE* 4.0 10.8 - - + +
100B ASP* 2.8 20.0 + - - +
101B PHE* 3.7 24.9 - - + -
126B LEU* 3.9 13.2 - - + -
127B VAL 3.3 13.0 - - - +
128B LEU* 3.8 14.9 - - + +
133B LYS* 1.3 82.2 - - - +
135B VAL* 1.3 66.2 + - - +
154B ILE* 4.0 21.5 - - + -
192B LEU* 4.3 6.7 - - + -
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Residues in contact with VAL 135 (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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101B PHE* 4.2 4.0 - - - -
125B TRP 3.7 0.2 - - - +
126B LEU* 3.7 5.8 - - - +
127B VAL* 2.9 54.4 + - + +
129B ASN* 3.9 31.4 - - + +
133B LYS* 3.9 11.0 - - + +
134B LEU* 1.3 80.9 - - - +
136B ILE* 1.3 65.8 + - - +
137B LEU* 3.8 16.4 + - + -
150B THR 4.9 1.8 - - - +
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Residues in contact with ILE 136 (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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101B PHE* 3.8 17.6 - - + -
107B PHE* 3.7 35.0 - - + -
110B GLU* 3.7 20.0 - - + -
111B PHE* 3.6 49.6 - - + +
114B VAL* 3.8 30.5 - - + -
125B TRP 3.4 4.7 - - - +
126B LEU* 4.6 0.4 - - + -
135B VAL* 1.3 76.6 - - - +
137B LEU* 1.3 69.9 + - - +
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Residues in contact with LEU 137 (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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114B VAL* 4.3 1.6 - - - +
124B GLY* 3.5 3.1 - - - -
125B TRP* 2.7 47.3 + - + +
127B VAL* 3.8 33.2 - - + -
135B VAL* 3.8 12.3 + - + -
136B ILE* 1.3 90.2 - - - +
138B GLN* 1.3 63.4 + - - +
139B THR* 5.3 2.2 - - + -
145B PRO* 4.1 6.1 - - + -
150B THR* 3.1 40.6 - - + +
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Residues in contact with GLN 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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114B VAL* 3.8 29.5 + - + +
117B GLY 5.0 0.7 - - - -
118B HIS* 2.7 45.2 + - + +
123B TRP 3.2 12.3 - - - +
124B GLY* 4.8 0.2 - - - -
125B TRP* 4.4 0.2 - - - -
137B LEU* 1.3 76.2 - - - +
139B THR* 1.3 69.1 + - - +
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Residues in contact with THR 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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118B HIS* 3.2 12.6 - - - -
122B GLY* 3.3 0.2 - - - -
123B TRP* 2.9 35.7 + - - +
125B TRP* 3.0 28.1 + - + +
137B LEU* 5.3 4.3 - - + -
138B GLN* 1.3 80.1 - - - +
140B HIS* 1.3 60.6 + - - +
143B GLY* 2.6 32.6 + - - +
144B ASN* 3.9 13.9 - - - -
145B PRO* 4.5 3.1 - - + -
148B ASP* 4.0 14.6 - - - +
150B THR* 6.0 0.2 - - - +
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Residues in contact with HIS 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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140A HIS* 4.1 2.5 - + - -
141A ASP* 2.6 37.5 + - - -
118B HIS* 2.9 23.6 + - + +
119B PHE* 3.1 24.0 + + - -
121B SER 3.0 14.9 + - - -
139B THR* 1.3 75.3 - - - +
141B ASP* 1.3 86.2 + - - +
142B ALA 3.1 0.5 + - - -
143B GLY* 2.9 24.0 + - - -
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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