Contacts of the strand formed by residues 161 - 167 (chain B) in PDB entry 3U7X
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 ASP 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B THR* 4.3 0.2 - - - -
117B LEU* 2.7 41.0 + - + +
118B ASN 4.9 2.9 + - - +
119B LYS* 5.9 0.2 - - - -
122B ARG* 2.8 66.0 + - - +
126B LEU* 3.7 28.1 - - + +
155B ASN 3.3 9.9 - - - +
156B VAL* 3.4 4.3 - - - -
157B ARG 3.1 12.2 + - - +
160B GLY* 1.3 75.6 - - - -
162B LYS* 1.3 62.2 + - - +
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Residues in contact with LYS 162 (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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112B ARG* 5.1 11.7 - - - +
114B LEU* 3.9 23.8 - - + -
115B ILE 3.3 5.8 - - - +
116B THR* 4.3 20.0 - - + -
154B VAL* 3.3 4.5 - - - +
155B ASN* 2.8 56.9 + - - +
157B ARG* 4.9 1.8 - - - -
160B GLY 3.9 9.2 + - - +
161B ASP* 1.3 81.2 - - - +
163B ILE* 1.3 63.1 + - - +
219B SO4 2.8 42.1 + - - -
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Residues in contact with ILE 163 (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 LEU* 3.7 1.9 - - - +
115B ILE* 2.8 44.9 + - + +
117B LEU* 4.3 9.6 - - + -
126B LEU* 3.8 20.4 - - + +
129B PHE* 3.5 33.2 - - + -
130B TRP* 3.7 28.5 - - + +
133B THR* 3.7 12.8 - - + +
153B VAL 3.3 3.8 - - - +
154B VAL* 3.9 14.8 - - + -
162B LYS* 1.3 78.6 - - - +
164B ALA* 1.3 65.2 + - - +
183B TYR* 3.3 22.7 - - - +
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Residues in contact with ALA 164 (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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112B ARG* 3.9 32.3 - - + +
113B TRP 3.1 12.8 - - - +
114B LEU* 4.0 9.2 - - + -
152B ALA* 3.1 9.0 - - - +
153B VAL* 2.9 35.5 + - + +
155B ASN* 6.0 1.3 - - - +
162B LYS* 6.2 0.2 - - + -
163B ILE* 1.3 79.3 - - - +
165B ILE* 1.3 62.0 + - - +
166B TRP* 3.9 8.8 + - + +
183B TYR* 4.7 1.3 - - - -
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Residues in contact with ILE 165 (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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112B ARG* 3.2 2.8 - - - -
113B TRP* 3.0 35.6 + - + +
133B THR* 3.8 20.2 - - + -
136B CYS* 4.9 1.1 - - + -
137B LEU* 3.9 16.2 - - + -
142B PHE* 3.7 22.2 - - + -
149B VAL* 4.2 13.7 - - + -
151B GLY 3.6 8.5 - - - +
152B ALA* 4.4 0.4 - - + -
164B ALA* 1.3 73.2 - - - +
166B TRP* 1.3 71.1 + - - +
167B THR* 4.0 6.6 + - + +
179B ILE* 4.3 16.8 - - + -
183B TYR* 3.6 42.9 - - + -
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Residues in contact with TRP 166 (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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94B PHE* 3.4 30.7 - + + -
100B PRO 4.2 11.4 - - - -
101B MET* 3.7 6.7 - - - -
102B TRP* 3.5 44.0 - + + -
107B ASN* 3.7 10.8 - - - +
111B GLY 3.4 5.8 - - - +
112B ARG* 3.7 30.9 - - + +
149B VAL* 3.7 4.0 - - - -
150B CYS* 2.8 25.4 + - + -
151B GLY 2.7 19.2 + - - +
153B VAL* 3.6 29.5 - - + +
164B ALA* 4.0 12.9 - - + +
165B ILE* 1.3 74.0 - - - +
167B THR* 1.3 60.7 + - - +
200B HIS* 3.5 24.7 - + - +
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Residues in contact with THR 167 (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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106B LYS 4.6 0.7 - - - +
107B ASN* 4.7 1.7 - - - +
110B GLY* 3.2 3.1 - - - -
111B GLY 2.9 27.9 + - - +
113B TRP* 4.8 2.7 - - + +
148B ASP* 3.1 20.6 - - - +
149B VAL* 4.6 1.8 - - - -
150B CYS* 3.7 5.9 - - - +
165B ILE* 4.4 14.8 - - + +
166B TRP* 1.3 80.0 - - - +
168B THR* 1.3 59.8 + - - +
169B GLU 4.1 2.8 + - - -
176B VAL* 4.0 10.7 - - + +
179B ILE* 3.9 27.1 - - + -
197B TYR* 2.7 37.7 + - + -
200B HIS* 4.7 2.3 + - - -
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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