Contacts of the helix formed by residues 177 - 186 (chain B) in PDB entry 5HK1
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 VAL 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B LEU 4.4 2.2 - - - -
121B TRP* 3.0 26.8 + - + +
122B ALA* 4.3 0.2 - - - +
176B GLY* 1.3 67.0 - - - -
178B ILE* 1.3 61.3 + - - +
179B PRO* 4.3 8.7 - - + -
180B SER* 2.6 48.9 + - - +
181B THR* 3.3 9.7 - - - +
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Residues in contact with ILE 178 (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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99B SER 3.8 6.5 - - - +
101B SER 3.5 31.2 - - - +
102B GLU 3.5 5.2 - - - +
103B TYR* 3.6 31.0 - - + -
122B ALA* 4.9 4.7 - - + -
174B GLY 3.9 6.3 - - - +
175B ARG 4.5 0.4 - - - -
176B GLY 2.8 29.5 + - - +
177B VAL* 1.3 70.8 - - - +
179B PRO* 1.4 71.5 - - + +
181B THR* 2.7 24.3 + - - +
182B LEU* 3.2 6.2 + - - +
206B TYR* 3.7 15.0 - - + +
301B 61W 3.8 30.1 - - + -
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Residues in contact with PRO 179 (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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100B LEU* 3.9 24.9 - - + +
177B VAL* 3.5 11.7 - - + -
178B ILE* 1.4 94.1 - - + +
180B SER* 1.3 59.7 + - - +
182B LEU* 3.2 22.1 + - + +
183B ALA* 3.6 5.7 + - - +
206B TYR* 3.7 22.7 - - + +
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Residues in contact with SER 180 (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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121B TRP* 3.7 34.8 - - - +
177B VAL* 2.6 39.8 + - - +
179B PRO* 1.3 77.4 - - - +
181B THR* 1.3 65.6 + - - +
183B ALA* 3.2 22.6 + - - +
184B PHE* 4.0 2.9 + - - +
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Residues in contact with THR 181 (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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103B TYR* 4.8 4.8 - - - -
120B TYR* 3.6 46.2 - - + +
121B TRP 4.6 1.3 - - - +
122B ALA* 4.0 15.7 - - + -
124B ILE* 5.5 3.1 - - + -
177B VAL 3.3 16.6 - - - +
178B ILE* 2.7 22.4 + - + +
180B SER* 1.3 77.8 - - - +
182B LEU* 1.3 62.6 + - - +
184B PHE* 3.3 15.0 + - - +
185B ALA* 3.4 12.4 + - - +
301B 61W 4.0 19.7 - - - -
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Residues in contact with LEU 182 (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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178B ILE 3.2 6.0 + - - +
179B PRO* 3.2 15.2 + - + +
180B SER 3.1 0.4 - - - -
181B THR* 1.3 80.4 + - - +
183B ALA* 1.3 60.5 + - - +
185B ALA* 3.3 15.4 + - + +
186B LEU* 3.4 35.9 + - + +
202B THR* 5.2 7.4 - - - +
203B LEU* 3.8 24.9 - - + -
206B TYR* 3.6 33.9 - - + -
301B 61W 3.6 34.3 - - + -
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Residues in contact with ALA 183 (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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194A GLN* 3.2 28.9 + - - +
179B PRO 3.6 4.6 + - - +
180B SER* 3.2 15.8 + - - +
181B THR 3.2 0.4 - - - -
182B LEU* 1.3 79.7 - - - +
184B PHE* 1.3 60.6 + - - +
186B LEU* 4.2 4.1 - - - +
187B ALA* 3.6 9.7 + - - -
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Residues in contact with PHE 184 (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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192A SER 4.0 6.3 - - - -
193A THR* 3.2 42.2 - - - -
194A GLN* 3.4 12.1 + - + +
86B ALA* 3.3 21.4 - - + +
87B GLY* 3.8 13.0 - - - -
89B TRP* 4.1 7.4 - + - -
116B HIS 3.5 23.1 - - - -
117B SER 3.3 7.4 - - - -
118B GLY* 3.6 11.7 - - - -
119B ARG 5.3 2.9 - - - +
120B TYR* 3.2 41.5 - + + -
180B SER 4.0 2.0 + - - +
181B THR* 3.3 9.9 + - - +
182B LEU 3.2 0.6 - - - -
183B ALA* 1.3 77.1 - - - +
185B ALA* 1.3 62.9 + - + +
186B LEU 3.0 9.3 + - - -
187B ALA* 3.2 14.6 + - - +
301B 61W 5.6 0.7 - - - -
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Residues in contact with ALA 185 (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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84B VAL* 4.1 15.6 - - + +
85B ASN 3.5 12.3 + - - +
86B ALA* 3.7 13.6 - - - +
89B TRP* 6.1 0.4 - - + -
120B TYR* 6.2 0.4 - - + -
181B THR 3.4 8.3 + - - +
182B LEU* 3.3 19.5 + - + +
184B PHE* 1.3 81.9 - - + +
186B LEU* 1.3 64.7 + - + +
187B ALA 3.6 0.4 - - - -
189B THR* 3.9 2.6 + - - -
301B 61W 4.4 30.1 - - + +
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Residues in contact with LEU 186 (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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182B LEU* 3.4 39.0 + - + +
183B ALA* 4.2 4.7 - - - +
184B PHE 3.0 0.8 - - - -
185B ALA* 1.3 84.5 - - + +
187B ALA* 1.3 65.2 + - - +
188B ASP 3.6 1.3 - - - -
189B THR* 3.4 16.0 + - + +
190B VAL* 3.2 28.4 + - + +
199B LEU* 3.6 33.2 - - + -
202B THR* 3.4 31.4 - - + +
203B LEU* 4.1 14.4 - - + -
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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