Contacts of the strand formed by residues 161 - 167 (chain B) in PDB entry 5H15
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 PRO 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B ASN* 4.5 9.6 - - - +
152B TRP* 4.4 10.8 - - + -
153B THR 3.7 7.4 - - - +
154B TYR* 4.3 1.6 - - - -
159B SER 3.7 1.3 - - - +
160B HIS* 1.4 105.2 - - + +
162B LEU* 1.3 61.4 + - - +
177B PRO* 3.0 34.7 - - + +
178B ILE* 4.4 6.1 - - + -
65D ILE* 4.3 10.5 - - + -
66D GLN* 3.3 36.1 - - + +
68D VAL* 4.2 11.9 - - + -
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Residues in contact with LEU 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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152B TRP* 3.4 10.0 - - - -
153B THR* 2.8 53.3 + - + +
154B TYR 4.1 3.4 - - - +
155B ASP* 3.8 32.1 - - + +
160B HIS* 4.0 13.5 - - + +
161B PRO* 1.3 81.7 - - - +
163B LEU* 1.3 60.0 + - - +
174B ILE* 4.2 18.4 - - + -
175B ILE 3.7 9.6 - - - +
176B ASN* 4.7 0.4 - - - -
177B PRO* 3.7 1.6 - - - -
183B ILE* 3.6 31.4 - - + -
184B LYS* 6.1 2.5 - - - -
220B ILE* 4.6 8.3 - - + -
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Residues in contact with LEU 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 ALA* 3.7 17.3 - - + -
121B VAL* 3.7 29.6 - - + -
123B LEU* 4.1 12.3 - - + -
150B CYS* 4.2 7.6 - - + -
151B ALA 3.4 25.1 - - - +
152B TRP* 3.6 39.5 - - + +
153B THR* 5.9 0.2 - - - -
162B LEU* 1.3 76.6 - - - +
164B ALA* 1.3 59.4 + - - +
165B VAL* 4.1 8.9 + - + -
173B ARG 3.6 1.4 - - - +
174B ILE* 3.6 2.8 - - - -
175B ILE* 2.8 48.3 + - + +
177B PRO* 4.9 4.7 - - + -
180B MET* 6.0 0.4 - - + -
198B PHE* 5.5 0.2 - - - -
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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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150B CYS* 3.1 5.2 - - - +
151B ALA 2.8 32.9 + - - +
162B LEU 4.4 0.2 - - - -
163B LEU* 1.3 72.0 - - - +
165B VAL* 1.3 61.9 + - - +
172B ILE* 4.5 1.1 - - + -
173B ARG 3.3 6.5 - - - +
174B ILE* 3.7 24.0 - - + -
196B LEU* 3.7 16.6 - - + +
198B PHE* 3.8 22.9 - - + -
206B LEU* 4.2 6.3 - - + -
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Residues in contact with VAL 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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116B VAL* 4.0 1.6 - - + -
121B VAL* 3.6 38.8 - - + -
147B PHE* 3.6 25.6 - - + -
149B THR 3.4 9.9 - - - +
150B CYS* 3.6 17.3 - - + -
163B LEU* 4.2 7.9 - - + +
164B ALA* 1.3 77.6 - - - +
166B ALA* 1.3 62.8 + - - +
171B ILE 3.7 0.5 - - - +
172B ILE* 3.6 1.4 - - - -
173B ARG* 2.9 38.2 + - + +
175B ILE* 3.8 20.0 - - + -
196B LEU* 3.6 3.5 - - - +
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Residues in contact with ALA 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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147B PHE* 3.7 10.2 - - - -
148B TYR 2.9 18.4 + - - -
149B THR* 3.3 17.6 + - + +
165B VAL* 1.3 79.5 - - - +
167B GLY* 1.3 59.8 + - - +
171B ILE 3.6 17.0 - - - +
172B ILE* 4.2 2.7 - - - -
193B ILE* 3.7 34.8 - - + -
196B LEU* 3.7 12.1 - - + +
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Residues in contact with GLY 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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145B GLU* 3.7 4.2 + - - -
146B ASN 3.1 14.1 - - - -
147B PHE* 4.0 3.2 - - - -
148B TYR* 3.7 12.1 - - - -
166B ALA* 1.3 77.3 - - - +
168B SER* 1.3 63.1 + - - -
169B ARG 3.3 2.9 - - - -
170B GLY* 3.1 8.9 + - - +
171B ILE 4.5 3.2 + - - -
193B ILE 2.9 30.2 + - - -
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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