Contacts of the strand formed by residues 156 - 164 (chain B) in PDB entry 1H1B
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 GLN 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.8 20.3 + - + +
19B GLY* 4.1 10.3 + - - +
20B ARG* 3.4 22.9 - - - +
21B ARG* 3.4 27.3 - - - +
22B ALA* 4.8 0.2 - - - -
139B MET* 3.2 28.5 - - - +
140B GLY 3.2 19.0 + - - +
144B LEU* 4.3 29.0 - - + +
152B ALA* 4.4 5.6 - - + +
154B VAL* 3.0 21.0 + - - +
155B LEU* 1.3 76.8 - - - +
157B GLU* 1.3 61.6 + - - +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.6 2.2 - - - -
19B GLY* 3.3 4.9 - - - -
20B ARG* 2.9 75.7 + - + +
21B ARG 4.5 0.2 - - - -
22B ALA* 3.2 21.5 - - + +
23B ARG 4.4 2.0 + - - -
26B ALA* 5.0 0.9 - - - +
27B TRP* 3.2 28.7 + - - +
137B LEU* 3.9 18.9 - - + +
138B ALA 3.2 11.2 - - - +
139B MET* 4.2 4.0 - - + +
156B GLN* 1.3 75.0 - - - +
158B LEU* 1.3 62.1 + - - +
1E NAG 5.7 0.7 - - - +
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Residues in contact with LEU 158 (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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16B ILE* 3.9 15.5 - - + -
17B VAL 4.2 1.1 - - - +
18B GLY 3.5 25.6 - - - +
19B GLY* 3.8 7.4 - - - -
20B ARG* 5.1 2.9 - - - +
137B LEU* 3.4 6.5 - - - +
138B ALA* 2.8 40.6 + - + +
157B GLU* 1.3 76.9 - - - +
159B ASN* 1.3 74.3 + - - +
160B VAL* 3.6 10.0 + - + +
185B VAL* 3.8 12.6 - - + -
187B ARG* 3.8 13.9 - - - +
188B ALA* 4.7 0.4 - - + -
189B GLY* 3.5 41.1 - - - +
190B VAL* 5.7 0.7 - - + -
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Residues in contact with ASN 159 (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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20B ARG* 2.4 43.2 + - - +
135B GLN* 5.4 8.3 + - + +
136B CYS 3.6 8.2 + - - +
137B LEU* 4.1 2.2 - - - +
158B LEU* 1.3 81.8 - - - +
160B VAL* 1.3 65.2 + - - +
185B VAL* 3.7 10.7 - - - +
187B ARG* 5.6 0.3 + - - -
1E NAG 1.5 65.9 + - + +
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Residues in contact with VAL 160 (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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135B GLN* 3.8 8.4 - - - +
136B CYS* 3.0 37.7 + - + +
138B ALA* 4.5 6.7 - - + -
158B LEU* 3.8 21.5 - - + +
159B ASN* 1.3 81.3 - - - +
162B THR* 1.3 68.1 + - - +
183B THR* 3.4 39.0 - - + +
184B LEU* 3.8 9.9 - - - +
185B VAL* 3.7 17.3 - - + +
189B GLY* 5.7 1.1 - - - -
190B VAL* 6.5 0.4 - - + -
199B LEU* 4.1 14.6 - - + -
226B ASP* 6.0 1.1 - - - +
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Residues in contact with THR 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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133B GLY* 3.8 13.0 - - - +
134B VAL 3.4 7.0 - - - +
135B GLN* 2.8 32.8 + - - +
160B VAL* 1.3 80.1 - - - +
163B VAL* 1.3 77.9 + - - +
164B VAL* 3.5 2.8 + - - +
183B THR* 3.2 4.7 - - - -
184B LEU 3.0 32.8 + - - -
186B ARG* 4.1 31.6 + - - +
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Residues in contact with VAL 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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130B LEU* 3.9 37.9 - - + +
131B GLY 3.9 23.8 - - - +
132B ASN* 2.9 17.9 + - - +
133B GLY 3.0 8.0 + - - -
134B VAL* 3.0 18.5 + - + +
136B CYS* 3.7 27.8 - - - -
162B THR* 1.3 74.1 - - - +
164B VAL* 1.3 67.6 + - - +
165B THR* 5.9 1.1 - - + -
181B VAL* 4.8 9.4 - - + -
182B CYS 3.3 12.3 - - - +
183B THR* 4.4 3.1 - - + +
201B CYS* 4.7 0.2 - - - -
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Residues in contact with VAL 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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132B ASN* 3.5 7.6 - - - +
162B THR* 3.9 9.9 - - + +
163B VAL* 1.3 85.1 - - - +
165B THR* 1.3 66.2 + - - +
166B SER* 3.3 31.6 - - - +
168B CYS* 4.1 2.8 - - - +
182B CYS* 2.8 31.0 + - - +
184B LEU* 4.2 18.4 - - + -
186B ARG* 3.7 29.2 - - - +
225B PRO* 4.3 14.1 - - + -
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Residues in contact with THR 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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129B ARG* 6.4 0.4 - - - +
130B LEU 4.9 9.6 - - - +
131B GLY* 5.7 0.2 - - - -
132B ASN* 3.6 33.3 + - - +
163B VAL* 5.9 0.7 - - + -
164B VAL* 1.3 75.5 - - - +
166B SER* 1.3 69.6 + - - +
167B LEU 3.3 1.9 + - - -
168B CYS* 3.3 21.0 + - + +
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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