Contacts of the helix formed by residues 163 - 172 (chain K) in PDB entry 5A31
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 CYS 163 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13J TYR* 3.0 27.1 + - + +
18J GLN* 4.9 4.0 - - + +
21J SER* 3.7 7.0 - - - +
130K SER* 5.9 2.2 - - - -
131K SER* 6.2 2.2 - - - -
134K LEU* 4.4 13.5 - - - -
156K ALA* 5.4 4.9 - - - -
157K LEU* 4.4 8.1 - - - +
160K ASP* 3.8 21.7 - - + +
161K VAL 3.2 7.8 + - - +
162K TYR* 1.3 71.4 - - - +
164K PHE* 1.3 60.0 + - - +
165K GLU* 4.1 8.7 - - - -
166K ALA* 3.9 30.1 + - - +
167K PHE 4.0 4.7 + - - -
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Residues in contact with PHE 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J GLN* 4.7 15.0 - - - -
21J SER* 3.7 6.0 + - - +
24J PHE* 3.5 70.2 - + + -
25J TRP* 4.4 0.9 - - + +
162K TYR 3.2 7.8 + - - +
163K CYS* 1.3 72.2 - - - +
165K GLU* 1.3 63.5 + - - +
166K ALA 3.2 0.9 - - - -
167K PHE* 3.1 13.7 + + - -
168K ASP* 2.7 65.5 + - + -
205K PHE* 4.2 18.2 - + + -
208K LYS* 4.0 22.7 - - + -
232K ASP* 5.7 2.0 - - - -
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Residues in contact with GLU 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J GLN 5.2 0.3 - - - +
18J GLN* 3.9 16.8 + - - +
19J TYR 3.9 6.8 + - - -
20J GLN* 3.2 35.5 + - + +
21J SER* 3.2 31.9 - - - +
78K ARG* 5.9 0.2 + - - -
134K LEU* 4.2 13.7 - - + -
138K LYS* 3.8 27.7 + - - -
163K CYS* 3.2 2.9 - - - -
164K PHE* 1.3 84.2 - - - +
166K ALA* 1.3 57.4 + - - +
168K ASP* 3.6 3.6 + - - +
169K LEU* 3.1 34.7 + - - +
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Residues in contact with ALA 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K LEU* 4.2 15.0 - - + -
153K TYR* 4.2 26.6 - - + +
156K ALA* 4.3 6.3 - - + -
157K LEU* 3.7 18.2 - - + +
163K CYS* 3.9 18.5 + - - +
164K PHE 3.2 0.2 - - - -
165K GLU* 1.3 77.5 - - - +
167K PHE* 1.3 65.4 + - - +
169K LEU* 3.3 4.0 + - - +
170K LEU* 3.1 25.1 + - - +
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Residues in contact with PHE 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K LEU* 3.5 29.3 - - + +
163K CYS 4.0 2.6 + - - +
164K PHE* 3.1 25.5 + + - +
166K ALA* 1.3 76.6 - - - +
168K ASP* 1.3 68.5 + - - +
170K LEU* 3.3 8.0 + - + +
171K THR* 3.0 51.5 + - + +
184K LEU* 5.7 5.4 - - + -
185K LEU* 3.5 27.6 - - + -
188K LEU* 5.4 3.1 - - + -
205K PHE* 3.5 51.6 - + + -
208K LYS* 4.5 15.5 - - + -
209K LEU* 4.0 11.9 - - + -
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Residues in contact with ASP 168 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J GLN* 4.7 10.4 + - - +
164K PHE* 2.7 53.6 + - + +
165K GLU* 4.1 4.3 - - - +
167K PHE* 1.3 75.0 - - - +
169K LEU* 1.3 58.0 + - - +
171K THR* 4.3 5.7 - - - +
172K SER* 2.9 54.4 + - - -
208K LYS* 4.6 9.4 - - - +
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Residues in contact with LEU 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K LEU* 4.9 0.7 - - + -
138K LYS* 4.4 18.4 - - + -
141K ASP* 3.6 9.6 - - - +
153K TYR* 3.1 53.8 - - + +
165K GLU* 3.1 19.5 + - - +
166K ALA 3.4 10.1 - - - +
168K ASP* 1.3 78.7 - - - +
170K LEU* 1.3 61.5 + - - +
172K SER* 4.1 6.7 + - - -
175K MET* 3.9 15.5 - - + +
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Residues in contact with LEU 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K THR* 3.4 37.9 - - - +
153K TYR* 4.0 13.6 - - + -
154K LYS* 4.3 13.9 - - + -
157K LEU* 3.6 30.5 - - + -
166K ALA 3.1 7.7 + - - +
167K PHE* 3.4 9.2 - - + +
169K LEU* 1.3 79.4 - - - +
171K THR* 1.3 58.5 + - - +
172K SER 3.7 0.2 - - - -
175K MET* 3.4 22.9 - - + +
176K LEU* 3.3 35.5 - - + +
184K LEU* 3.6 24.2 - - + -
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Residues in contact with THR 171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167K PHE* 3.0 54.1 + - + +
168K ASP* 4.3 6.5 - - - +
170K LEU* 1.3 76.5 - - - +
172K SER* 1.3 67.0 + - - +
173K HIS 3.4 1.7 + - - -
174K HIS 3.5 9.5 + - - -
175K MET 4.2 2.2 + - - -
176K LEU* 3.7 19.9 - - - +
181K GLU* 4.3 5.9 + - - -
208K LYS* 5.0 8.2 + - + -
209K LEU* 3.1 24.7 - - + +
211K LYS* 4.0 9.7 + - - -
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Residues in contact with SER 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K ASP* 2.9 47.7 + - - -
169K LEU* 4.1 6.2 + - - -
170K LEU 3.7 1.6 - - - -
171K THR* 1.3 74.2 - - - +
173K HIS* 1.3 88.0 + - - +
174K HIS 3.2 0.7 + - - -
175K MET* 3.6 20.6 + - - +
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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