Contacts of the helix formed by residues 165 - 180 (chain B) in PDB entry 3C51
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 SER 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.7 13.3 - - - +
173A GLN* 5.6 0.4 - - - +
75B PHE* 4.2 11.3 - - - -
161B GLU 3.8 6.5 - - - -
162B PHE* 3.1 21.0 + - - -
163B LEU 3.3 3.5 + - - +
164B ASP* 1.3 77.8 - - - +
166B LEU* 1.3 64.5 + - - +
167B TYR* 2.9 21.7 + - - +
168B PHE* 3.4 12.5 + - - +
169B LEU* 3.5 14.0 + - - +
566B BR 4.0 15.7 - - - -
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Residues in contact with LEU 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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44A LEU* 4.0 15.3 - - + -
166A LEU* 3.8 23.3 - - + +
169A LEU* 3.6 30.1 - - + -
170A ARG* 3.1 44.6 - - + +
173A GLN* 3.2 15.9 - - - +
531A TRP* 3.6 21.5 - - + -
165B SER* 1.3 72.0 + - - +
167B TYR* 1.3 61.8 + - - +
169B LEU* 3.0 7.3 + - - +
170B ARG* 2.9 28.4 + - - +
531B TRP* 4.5 4.7 - - + -
566B BR 3.6 9.2 - - + +
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Residues in contact with TYR 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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170A ARG* 4.8 1.4 + - - -
530A VAL 3.0 20.8 + - - -
531A TRP* 3.0 72.2 + + - -
71B LEU* 3.5 19.6 - - + +
74B GLN* 4.0 19.1 - - + -
75B PHE* 3.7 18.4 - + + -
78B THR* 3.1 25.7 + - + +
79B HIS* 4.9 1.1 - + - -
162B PHE* 3.8 17.9 - - + -
165B SER* 2.9 13.1 + - - +
166B LEU* 1.3 77.1 - - - +
168B PHE* 1.3 57.4 + - - +
170B ARG* 3.2 1.9 + - - +
171B PHE* 2.8 24.6 + - - +
566B BR 4.1 17.9 - - + -
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Residues in contact with PHE 168 (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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51B ARG* 4.2 26.2 - - + -
61B MET* 3.6 35.9 - - + -
162B PHE* 3.2 33.9 - + + +
163B LEU* 3.0 46.0 - - + +
165B SER* 3.4 5.8 + - - +
166B LEU 3.3 0.4 - - - -
167B TYR* 1.3 80.1 - - - +
169B LEU* 1.3 65.9 + - + +
171B PHE* 3.0 30.8 + + - +
172B LEU* 3.1 35.7 + - + +
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Residues in contact with LEU 169 (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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44A LEU* 3.5 17.3 - - + -
166A LEU* 3.5 15.3 - - + -
169A LEU* 3.2 34.8 - - + -
44B LEU* 3.9 14.1 - - + +
47B CYS* 5.0 0.7 - - - -
51B ARG* 4.1 31.9 - - - +
163B LEU 5.5 0.4 - - - +
165B SER 3.5 10.7 + - - +
166B LEU* 3.0 8.6 + - + +
168B PHE* 1.3 81.3 - - + +
170B ARG* 1.3 60.7 + - - +
172B LEU* 3.3 11.9 + - + +
173B GLN* 3.0 31.0 + - - +
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Residues in contact with ARG 170 (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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166A LEU* 3.0 26.2 - - + +
167A TYR* 5.4 1.8 + - - -
531A TRP* 3.8 24.8 - - + -
41B LEU* 3.7 16.5 - - - +
71B LEU* 3.7 10.8 - - + -
166B LEU 2.9 12.3 + - - +
167B TYR 3.5 7.9 - - - +
169B LEU* 1.3 73.1 - - - +
171B PHE* 1.3 66.5 + - - +
173B GLN* 3.0 26.9 + - - +
174B TRP* 3.0 44.2 + - + +
528B LEU 4.3 0.4 + - - -
529B ASN* 3.4 43.9 + - - +
530B VAL 4.2 12.1 + - - -
531B TRP* 5.0 5.9 - - - -
565B BR 3.5 17.6 - - - +
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Residues in contact with PHE 171 (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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56B LEU* 3.4 24.5 - - + -
61B MET* 3.1 44.6 - - + -
65B GLN* 4.1 9.6 - - - -
67B ILE* 4.4 3.1 - - + -
68B GLY* 3.3 40.2 - - - -
71B LEU* 3.2 16.7 - - + +
162B PHE* 4.7 4.5 - + + -
167B TYR 2.8 13.3 + - - +
168B PHE* 3.0 23.8 + + + +
170B ARG* 1.3 76.4 - - - +
172B LEU* 1.3 62.1 + - + +
174B TRP* 3.2 7.6 + - + +
175B LYS* 3.0 46.9 + - + +
516B GLN* 5.0 1.3 - - - -
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Residues in contact with LEU 172 (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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47B CYS* 4.2 24.0 - - + +
50B LEU* 3.9 15.1 - - + +
51B ARG* 4.1 32.1 - - + +
54B LEU* 3.9 27.6 - - + -
61B MET* 5.6 0.4 - - + -
168B PHE* 3.1 45.6 + - + +
169B LEU* 3.7 12.3 - - + +
170B ARG 3.3 0.2 - - - -
171B PHE* 1.3 78.9 - - + +
173B GLN* 1.3 67.9 - - - +
174B TRP 3.0 1.8 - - - -
175B LYS* 2.8 14.8 + - - +
176B TRP* 2.8 14.7 + - - +
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Residues in contact with GLN 173 (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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166A LEU* 3.3 20.6 - - - +
41B LEU* 3.6 23.7 - - + +
42B PRO* 3.3 51.4 + - + +
44B LEU* 3.3 24.2 - - + +
47B CYS* 4.0 9.8 - - - -
169B LEU 3.0 15.4 + - - +
170B ARG* 3.0 36.2 + - - +
172B LEU* 1.3 76.4 - - - +
174B TRP* 1.3 60.0 + - - +
176B TRP* 3.5 0.9 - - - +
177B LEU* 3.3 14.0 + - - +
565B BR 3.8 9.8 - - - +
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Residues in contact with TRP 174 (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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41B LEU* 3.6 11.2 - - + +
67B ILE* 3.5 40.8 - - + -
71B LEU* 4.4 0.4 - - + -
170B ARG* 3.0 47.0 + - + +
171B PHE* 3.5 8.1 - - + +
172B LEU 3.0 0.6 - - - -
173B GLN* 1.3 74.3 - - - +
175B LYS* 1.3 61.3 + - + +
176B TRP 3.1 1.8 - - - -
177B LEU* 3.3 24.3 + - + +
178B GLU* 3.0 28.6 + - - +
515B TRP* 3.6 27.2 - + + -
516B GLN* 6.4 0.4 - - + -
519B MET* 4.0 10.1 - - + -
524B VAL* 4.1 2.2 - - + -
525B PHE* 3.4 48.2 - + - -
528B LEU* 3.7 36.1 - - + -
529B ASN* 4.2 4.3 + - - +
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Residues in contact with LYS 175 (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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50B LEU* 3.7 8.3 - - + +
54B LEU* 3.6 24.6 - - + +
56B LEU* 3.8 11.9 - - + +
65B GLN* 3.1 35.0 + - - +
171B PHE* 3.0 43.6 + - + +
172B LEU* 2.8 11.8 + - - +
174B TRP* 1.3 74.2 - - + +
176B TRP* 1.3 58.0 + - - +
178B GLU* 2.9 42.6 + - - +
179B ALA* 3.1 25.8 + - - +
512B PRO* 4.0 10.1 - - - +
516B GLN* 3.7 5.3 - - - +
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Residues in contact with TRP 176 (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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40B LYS 4.4 11.4 - - - -
42B PRO* 3.5 33.7 - - + -
46B LYS* 2.9 55.5 + - + +
47B CYS* 4.6 2.2 - - - -
50B LEU* 3.3 24.4 - - + +
172B LEU 2.8 7.2 + - - +
173B GLN* 3.5 9.2 - - - +
175B LYS* 1.3 74.6 - - - +
177B LEU* 1.3 86.4 + - + +
178B GLU 3.1 1.3 - - - -
179B ALA* 2.9 20.2 + - + +
180B GLN* 2.9 63.0 + - + +
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Residues in contact with LEU 177 (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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38B ARG 4.3 3.4 - - - +
39B LEU* 3.3 37.9 - - + -
40B LYS 3.0 46.0 - - - +
41B LEU* 4.2 3.4 - - + +
173B GLN 3.3 10.2 + - - +
174B TRP* 3.7 24.5 - - + +
176B TRP* 1.3 92.3 - - + +
178B GLU* 1.3 61.6 + - - +
180B GLN* 3.5 19.0 + - + +
182B MET* 4.7 6.8 - - - +
515B TRP* 3.5 19.7 - - + -
528B LEU* 4.6 3.4 - - + -
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Residues in contact with GLU 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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174B TRP 3.0 12.4 + - - +
175B LYS* 2.9 48.2 + - - +
177B LEU* 1.3 78.3 - - - +
179B ALA* 1.3 60.9 + - - +
180B GLN 3.2 4.5 + - - +
182B MET* 3.9 2.1 - - - +
510B THR* 3.0 33.8 - - + +
512B PRO* 3.5 28.3 - - + +
515B TRP* 3.5 39.6 - - + -
516B GLN* 3.5 14.9 + - - +
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Residues in contact with ALA 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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50B LEU* 5.0 12.3 - - + -
175B LYS 3.1 10.7 + - - +
176B TRP* 2.9 12.7 + - + +
178B GLU* 1.3 79.3 - - + +
180B GLN* 1.3 69.5 + - - +
181B PRO* 3.8 1.2 - - - +
510B THR* 5.0 3.5 - - - +
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Residues in contact with GLN 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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176B TRP* 2.9 78.1 + - + +
177B LEU* 3.5 14.6 - - + +
178B GLU 3.2 10.4 - - - +
179B ALA* 1.3 84.5 - - - +
181B PRO* 1.3 82.0 - - + +
182B MET* 3.4 10.3 + - + +
186B TRP* 6.3 1.8 - - + -
510B THR* 4.3 4.3 - - - +
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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