Contacts of the strand formed by residues 133 - 140 (chain B) in PDB entry 2AW9
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 4.2 3.8 - - - -
131B GLY 3.7 1.8 + - - -
132B SER* 1.3 76.6 - - - +
134B TRP* 1.3 69.6 + - - -
149B THR 3.1 13.9 - - - -
151B ASN 3.6 13.5 - - - -
174B VAL* 2.9 31.6 + - - +
175B TRP* 3.3 9.2 + - - +
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Residues in contact with TRP 134 (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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80B ASN* 3.5 41.5 - - + +
81B HIS* 3.7 15.5 - + - -
84B PHE* 3.8 26.5 - + + -
129B ARG* 4.5 1.9 + - - +
133B GLY* 1.3 75.4 - - - -
135B ALA* 1.3 61.0 + - - +
136B TRP* 3.4 41.3 - + + +
148B SER* 3.1 8.1 - - - -
149B THR* 3.0 29.8 + - - +
151B ASN 3.1 20.2 + - - -
152B GLN* 3.0 17.5 + - - -
171B GLY 4.6 2.2 - - - -
172B VAL 3.4 13.5 - - - -
173B ASP* 3.4 53.2 - - + -
174B VAL* 4.5 4.7 - - - -
175B TRP* 3.8 7.9 - - - +
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Residues in contact with ALA 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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122B PHE* 3.8 10.3 - - + +
125B ALA* 4.3 7.6 - - + -
126B ALA* 3.8 40.2 - - + +
134B TRP* 1.3 73.7 - - - +
136B TRP* 1.3 65.2 + - - +
147B VAL 3.4 7.6 - - - +
148B SER* 4.1 0.7 - - - +
171B GLY* 3.0 5.5 - - - -
172B VAL* 2.9 38.8 + - + -
174B VAL* 5.2 0.4 - - + +
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Residues in contact with TRP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 3.2 35.4 - - + -
83B MET* 3.8 24.0 - - - -
122B PHE* 3.8 6.8 - - - -
134B TRP* 3.4 34.4 - + + +
135B ALA* 1.3 77.8 - - - +
137B LEU* 1.3 60.4 + - - +
138B VAL* 4.0 10.4 + - + -
145B ASP 3.9 0.2 - - - +
146B VAL* 3.3 9.2 - - - +
147B VAL* 2.6 51.6 + - + +
148B SER* 4.0 5.4 - - - -
149B THR* 3.1 30.6 + - + +
153B ASP 3.9 6.3 - - - -
154B ASN* 3.4 13.5 - - - -
155B PRO* 3.7 21.3 - - + -
168B PRO* 3.5 16.4 - - + -
170B LEU 3.2 5.6 - - - +
171B GLY* 3.6 21.5 - - - -
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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
----------------------------------------------------------
104B LEU* 5.1 1.1 - - + -
108B ILE* 5.0 6.5 - - + -
112B PHE* 4.1 8.7 - - + -
118B PHE* 4.0 36.3 - - + -
122B PHE* 3.8 1.9 - - + -
136B TRP* 1.3 71.8 - - - +
138B VAL* 1.3 60.5 + - - +
144B LEU* 4.0 30.7 - - + -
145B ASP 3.6 15.7 - - - +
146B VAL* 4.4 0.9 - - + +
168B PRO* 3.5 2.6 - - - +
169B ILE* 2.9 51.7 + - + +
170B LEU* 2.7 31.8 + - + +
200B TRP* 5.0 5.4 - - + -
203B VAL* 4.7 5.8 - - + -
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Residues in contact with VAL 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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136B TRP* 4.0 2.5 - - + -
137B LEU* 1.3 77.1 - - - +
139B VAL* 1.3 62.3 + - - +
140B LYS* 4.4 6.5 - - + -
144B LEU* 3.2 10.1 - - - +
145B ASP* 2.9 53.1 + - + +
147B VAL* 3.9 16.4 - - + -
155B PRO* 3.7 34.3 - - + -
165B SER 3.8 15.7 - - - +
166B GLY* 4.2 2.9 - - - -
167B THR 3.1 13.5 - - - +
168B PRO* 3.8 14.1 - - + -
169B ILE* 5.4 0.2 - - - -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 1.3 70.1 - - - +
140B LYS* 1.3 65.4 + - - +
142B GLY* 3.8 30.5 - - - +
143B LYS 3.4 3.8 - - - -
144B LEU* 3.7 21.3 - - + -
166B GLY* 3.4 1.7 - - - -
167B THR* 2.8 35.0 + - - +
169B ILE* 4.1 17.9 - - + -
207B TYR* 3.9 20.9 - - + +
210B ALA* 4.2 28.5 - - + +
211B LYS* 5.1 3.6 - - + +
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Residues in contact with LYS 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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138B VAL* 4.4 10.1 - - + -
139B VAL* 1.3 77.2 - - - +
141B ASP* 1.3 91.4 + - - +
143B LYS* 2.8 25.7 + - - +
145B ASP* 5.3 7.2 - - + -
165B SER* 2.9 37.1 + - - +
166B GLY* 4.1 9.4 - - - +
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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