Contacts of the helix formed by residues 165 - 180 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A PHE* 4.3 11.9 - - - -
161A GLU 3.7 7.0 - - - -
162A PHE* 2.4 29.1 + - - -
163A LEU 3.3 3.3 + - - +
164A ASP* 1.3 79.5 - - - +
166A LEU* 1.3 64.8 + - - +
167A TYR* 3.5 15.7 + - - +
168A PHE* 3.3 12.3 + - - +
169A LEU* 3.5 8.8 + - - +
44B LEU* 3.3 18.1 - - - +
565B BR 4.1 14.8 - - - -
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Residues in contact with LEU 166 (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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165A SER* 1.3 71.6 - - - +
167A TYR* 1.3 67.3 + - - +
169A LEU* 3.0 5.4 + - - +
170A ARG* 2.9 21.8 + - - +
531A TRP* 4.1 11.7 - - + -
44B LEU* 3.6 12.7 - - + +
166B LEU* 3.8 19.5 - - + +
169B LEU* 3.5 31.0 - - + -
170B ARG* 3.0 46.4 - - + +
173B GLN* 3.3 24.5 - - - +
531B TRP* 3.9 15.8 - - + -
565B BR 3.7 7.3 - - + +
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Residues in contact with TYR 167 (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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71A LEU* 3.9 19.6 - - + +
74A GLN* 4.1 15.0 - - + -
75A PHE* 3.4 33.2 - + + -
78A THR* 2.9 32.0 + - - +
79A HIS* 4.2 6.5 - + - -
162A PHE* 3.7 20.2 - - + -
165A SER* 3.1 6.7 - - - +
166A LEU* 1.3 78.3 - - - +
168A PHE* 1.3 58.5 + - - +
170A ARG* 2.9 5.7 + - - +
171A PHE* 2.7 27.5 + - - +
170B ARG* 5.4 2.2 + - - -
530B VAL 3.6 4.3 + - - -
531B TRP* 3.0 73.1 + + - -
565B BR 4.6 6.5 - - + -
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Residues in contact with PHE 168 (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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51A ARG* 4.5 19.1 - - + -
61A MET* 3.5 22.2 - - + -
162A PHE* 3.2 39.7 - + + +
163A LEU* 3.3 47.3 - - + +
165A SER* 3.3 9.4 + - - +
166A LEU 3.2 0.4 - - - -
167A TYR* 1.3 78.1 - - - +
169A LEU* 1.3 69.0 + - + +
171A PHE* 2.9 19.3 + + - +
172A LEU* 3.0 50.7 + - + +
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Residues in contact with LEU 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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44A LEU* 3.7 20.6 - - + +
47A CYS* 4.7 0.4 - - + -
51A ARG* 3.7 33.4 - - - +
163A LEU 5.8 0.7 - - - +
165A SER 3.8 9.0 - - - +
166A LEU 3.0 7.9 + - - +
168A PHE* 1.3 89.0 - - + +
170A ARG* 1.3 56.4 + - - +
172A LEU* 3.3 12.2 + - + +
173A GLN* 3.0 28.1 + - - +
44B LEU* 3.7 16.8 - - + -
166B LEU* 3.6 12.8 - - + -
169B LEU* 3.2 35.9 - - + -
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Residues in contact with ARG 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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41A LEU* 3.0 28.5 - - - +
71A LEU* 3.9 12.6 - - + -
166A LEU 2.9 12.2 + - - +
167A TYR 2.9 8.0 + - - +
169A LEU* 1.3 73.0 - - - +
171A PHE* 1.3 65.4 + - - +
173A GLN* 2.8 35.7 + - - +
174A TRP* 3.0 20.8 + - + +
528A LEU 4.7 1.3 + - - -
529A ASN* 3.0 46.7 + - - +
530A VAL 4.1 12.1 + - - +
531A TRP* 4.8 5.9 - - - -
166B LEU* 3.1 26.8 - - + +
167B TYR* 4.8 2.4 + - - -
531B TRP* 3.6 22.2 - - + +
566B BR 3.8 13.9 - - - +
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Residues in contact with PHE 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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54A LEU* 4.9 0.2 - - + -
56A LEU* 3.3 28.9 - - + -
61A MET* 3.2 44.0 - - + -
65A GLN* 3.7 9.9 - - - -
67A ILE* 4.4 7.4 - - + -
68A GLY* 3.7 34.1 - - - -
71A LEU* 3.5 13.6 - - + +
162A PHE* 4.6 6.5 - + + -
167A TYR 2.7 16.4 + - - +
168A PHE* 3.1 15.7 - + - +
170A ARG* 1.3 72.7 - - - +
172A LEU* 1.3 72.5 + - + +
174A TRP* 3.3 4.6 + - + +
175A LYS* 3.1 40.4 + - + +
516A GLN* 4.2 4.7 - - - -
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Residues in contact with LEU 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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44A LEU* 6.2 0.2 - - + -
47A CYS* 3.9 31.0 - - + +
50A LEU* 4.2 4.4 - - + +
51A ARG* 4.2 24.7 - - + +
54A LEU* 3.7 26.9 - - + -
168A PHE* 3.0 54.3 + - + +
169A LEU* 3.5 18.2 - - + +
170A ARG 3.2 0.2 - - - -
171A PHE* 1.3 79.3 - - + +
173A GLN* 1.3 67.6 + - - +
175A LYS* 2.8 17.8 + - - +
176A TRP* 2.8 14.6 + - - +
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Residues in contact with GLN 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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41A LEU* 3.9 14.3 - - + +
42A PRO* 2.4 57.5 + - + +
43A PRO* 4.4 5.7 - - - +
44A LEU* 4.6 10.9 - - + +
47A CYS* 3.8 10.0 - - - -
169A LEU 3.0 14.7 + - - +
170A ARG* 2.8 47.6 + - - +
172A LEU* 1.3 76.7 - - - +
174A TRP* 1.3 57.2 + - - +
176A TRP* 3.4 1.4 - - - +
177A LEU* 3.3 17.3 + - - +
164B ASP 5.6 0.6 + - - -
166B LEU* 3.2 16.3 - - - +
566B BR 3.6 20.2 - - - +
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Residues in contact with TRP 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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41A LEU* 3.8 11.4 - - + +
67A ILE* 3.4 37.2 - - + -
71A LEU* 4.3 0.2 - - + -
170A ARG* 3.0 46.3 + - + +
171A PHE* 3.7 7.2 - - + +
173A GLN* 1.3 74.0 - - - +
175A LYS* 1.3 59.9 + - - +
176A TRP 3.1 1.8 - - - -
177A LEU* 3.7 14.6 - - + +
178A GLU* 3.0 29.5 + - - +
515A TRP* 3.8 33.4 - + + -
516A GLN* 5.6 3.4 - - - +
519A MET* 4.0 12.3 - - + -
524A VAL 4.1 0.9 - - - -
525A PHE* 3.2 49.6 - + - -
528A LEU* 3.5 40.2 - - + -
529A ASN* 4.2 5.4 + - - +
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Residues in contact with LYS 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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50A LEU* 3.9 7.3 - - + +
54A LEU* 3.6 37.7 - - + +
56A LEU* 3.7 8.8 - - - +
65A GLN* 3.1 29.8 + - - +
171A PHE* 3.1 41.3 + - + +
172A LEU* 2.8 13.6 + - - +
174A TRP* 1.3 73.7 - - - +
176A TRP* 1.3 57.7 + - - +
178A GLU* 3.1 35.6 + - - +
179A ALA* 3.2 24.8 + - - +
512A PRO* 4.0 12.9 - - - +
516A GLN* 3.6 12.3 - - - +
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Residues in contact with TRP 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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40A LYS 4.0 5.6 - - - -
42A PRO* 3.3 39.3 - - + -
46A LYS* 3.2 57.5 + - + +
47A CYS* 4.8 1.3 - - - -
50A LEU* 3.4 19.0 - - + +
172A LEU 2.8 10.4 + - - +
173A GLN* 3.4 9.0 - - - +
175A LYS* 1.3 73.8 - - - +
177A LEU* 1.3 98.8 + - + +
178A GLU 3.1 1.6 - - - -
179A ALA* 2.8 25.6 + - + +
180A GLN* 3.1 45.5 + - + +
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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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38A ARG 4.4 4.3 - - - +
39A LEU* 4.1 28.5 - - + +
40A LYS 2.8 45.3 - - - +
41A LEU* 4.2 11.2 - - + -
173A GLN 3.3 10.8 + - - +
174A TRP* 3.7 34.1 - - + +
176A TRP* 1.3 96.8 - - + +
178A GLU* 1.3 63.1 + - - +
180A GLN* 3.3 20.5 + - + +
182A MET* 4.2 8.0 - - - +
515A TRP* 4.1 6.0 - - + -
528A LEU* 4.3 2.7 - - + -
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Residues in contact with GLU 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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174A TRP 3.0 16.9 + - - +
175A LYS* 3.1 31.4 + - - +
177A LEU* 1.3 76.0 - - - +
179A ALA* 1.3 63.5 + - - +
180A GLN 3.1 2.6 + - - +
182A MET* 3.2 19.1 - - - +
510A THR* 3.3 20.5 - - + +
512A PRO* 3.4 35.2 - - + +
515A TRP* 3.6 31.3 - - + -
516A GLN* 3.2 28.6 + - - +
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Residues in contact with ALA 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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50A LEU* 5.2 10.3 - - + -
175A LYS 3.2 10.9 + - - +
176A TRP* 2.8 18.3 + - + +
178A GLU* 1.3 73.9 - - - +
180A GLN* 1.3 71.4 + - - +
181A PRO* 3.9 1.2 - - - +
510A THR* 5.2 2.8 - - - +
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Residues in contact with GLN 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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176A TRP* 3.1 66.3 + - + +
177A LEU* 3.4 14.4 - - + +
178A GLU 3.1 10.4 + - - +
179A ALA* 1.3 85.1 + - - +
181A PRO* 1.3 81.7 - - + +
182A MET* 3.4 11.2 + - + +
510A THR* 4.0 3.8 - - - +
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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