Contacts of the helix formed by residues 168 - 180 (chain A) in PDB entry 3KVH
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 THR 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.0 23.8 - - + +
100A HIS* 4.5 8.3 - - + +
102A THR* 3.2 30.5 - - + +
110A ALA* 3.8 18.2 - - + -
166A VAL 3.2 0.8 + - - -
167A SER* 1.3 77.6 + - - +
169A ALA* 1.3 57.0 + - - +
170A LYS* 3.4 2.7 - - - -
171A CYS* 3.3 10.9 + - - +
172A GLN* 2.8 51.6 + - + +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A MET* 4.3 9.9 - - + +
60A LEU 4.2 3.6 - - - +
61A GLY* 3.9 17.9 - - - -
62A PHE* 3.6 8.6 - - + +
165A PHE* 4.5 2.0 - - + -
166A VAL* 3.0 31.1 + - + +
167A SER 3.2 2.8 + - - -
168A THR* 1.3 76.4 - - - +
170A LYS* 1.3 58.1 + - - +
172A GLN* 3.6 14.9 + - - +
173A LEU* 2.9 30.5 + - - +
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.0 41.7 + - + -
163A ASN 5.0 1.8 + - - -
165A PHE* 3.8 39.8 - - + +
166A VAL 4.4 0.2 + - - -
168A THR 3.4 0.6 - - - -
169A ALA* 1.3 78.7 - - - +
171A CYS* 1.3 65.3 + - - +
173A LEU* 3.3 6.9 + - - +
174A LEU* 3.1 34.9 + - + +
192A LEU* 3.6 31.4 - - - +
195A ALA* 5.2 1.8 - - - +
196A THR* 5.2 1.8 + - - -
199A GLN* 4.5 16.2 + - - +
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Residues in contact with CYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.0 29.8 - - + -
100A HIS* 6.3 0.4 - - - -
168A THR* 3.3 11.0 + - - +
170A LYS* 1.3 82.1 - - - +
172A GLN* 1.3 56.3 + - - +
174A LEU* 3.4 10.1 + - - +
175A PHE* 2.9 31.2 + - - +
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 4.7 13.4 + - - +
62A PHE* 3.9 15.6 - - + -
100A HIS* 4.9 10.9 + - - +
110A ALA* 3.6 33.1 + - - +
111A HIS 4.2 4.2 + - - -
112A LEU* 3.7 40.6 - - + +
168A THR* 2.8 33.9 + - + +
169A ALA* 3.6 18.4 + - - +
171A CYS* 1.3 70.7 - - - +
173A LEU* 1.3 60.5 + - - +
175A PHE* 3.3 5.3 + - - +
176A ALA* 2.9 32.7 + - - +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A MET* 4.4 8.1 - - - -
50A VAL* 4.4 13.5 - - + -
52A MET* 4.0 20.6 - - + -
62A PHE* 3.8 24.8 - - + -
145A VAL* 4.7 5.8 - - + -
157A PHE* 4.2 8.3 - - + -
160A PHE* 4.1 11.4 - - + -
161A LEU* 4.0 26.2 - - + -
165A PHE* 4.9 3.6 - - + -
169A ALA 2.9 17.4 + - - +
170A LYS* 3.3 5.4 + - - +
172A GLN* 1.3 77.3 - - - +
174A LEU* 1.3 59.5 + - - +
176A ALA* 3.7 2.7 - - - +
177A LEU* 2.9 55.2 + - + +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GOL 3.8 43.0 - - - +
157A PHE* 4.0 19.7 - - + -
161A LEU* 4.1 16.4 - - + -
170A LYS* 3.1 26.9 + - + +
171A CYS* 3.9 7.6 - - - +
173A LEU* 1.3 73.8 - - + +
175A PHE* 1.3 64.1 + - - +
177A LEU* 3.6 3.3 + - - -
178A LYS* 3.2 19.2 + - - +
188A LEU* 3.6 35.3 - - + +
192A LEU* 4.1 21.8 - - + -
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Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLN* 3.8 29.8 - - - -
97A LEU* 4.6 11.0 - - + -
98A SER* 3.8 19.5 - - - -
100A HIS* 4.4 18.8 - + + -
112A LEU* 4.5 11.4 - - + -
171A CYS 2.9 18.4 + - - +
172A GLN* 3.7 5.8 - - - +
174A LEU* 1.3 78.3 - - - +
176A ALA* 1.3 60.8 + - - +
178A LYS* 3.3 18.7 + - - +
179A VAL* 3.0 62.7 + - + +
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A MET* 3.4 31.2 - - + -
97A LEU* 3.8 22.2 - - + -
112A LEU* 4.1 4.5 - - + -
172A GLN 2.9 18.3 + - - +
173A LEU 3.7 0.4 - - - +
175A PHE* 1.3 74.9 - - - +
177A LEU* 1.3 66.0 + - - +
179A VAL* 4.0 9.0 - - - -
180A LEU* 2.9 32.6 + - + +
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A MET* 4.1 7.2 - - + -
50A VAL* 4.5 3.1 - - + -
147A LEU* 3.9 22.9 - - + -
157A PHE* 3.6 31.0 - - + -
173A LEU* 2.9 37.8 + - + +
174A LEU* 3.9 1.8 - - - +
175A PHE 3.4 0.2 - - - -
176A ALA* 1.3 75.0 - - - +
178A LYS* 1.3 59.5 + - - +
181A ASN 3.5 0.2 + - - -
182A MET* 2.9 66.7 + - + -
183A MET* 3.3 9.5 + - + -
188A LEU* 3.8 23.8 - - + -
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GOL 4.8 8.7 + - - +
174A LEU 3.2 10.9 + - - +
175A PHE* 3.5 19.9 - - - +
176A ALA 3.2 0.4 - - - -
177A LEU* 1.3 78.1 - - - +
179A VAL* 1.3 75.6 + - - +
181A ASN* 3.0 26.5 + - - +
183A MET 4.1 5.0 - - - +
185A GLU* 3.8 45.3 + - + +
188A LEU* 3.7 12.0 - - + +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 4.4 17.3 - - + -
175A PHE* 3.0 57.7 + - + +
176A ALA* 3.8 9.9 - - - +
178A LYS* 1.3 87.6 - - + +
180A LEU* 1.3 64.1 + - + +
181A ASN* 3.2 10.8 + - - +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A MET* 4.2 7.2 - - + -
33A TYR* 3.8 39.3 + - + +
97A LEU* 4.0 28.9 - - + -
114A ALA* 3.9 18.2 - - + -
176A ALA 2.9 19.8 + - - +
179A VAL* 1.3 77.9 - - + +
181A ASN* 1.3 71.1 + - - +
182A MET* 3.2 23.3 + - + +
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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