Contacts of the helix formed by residues 165 - 173 (chain B) in PDB entry 3AP1
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 4.1 24.3 - - - +
111B GLN* 3.1 34.8 + - - +
162B THR 2.9 13.0 + - - -
164B LYS* 1.3 77.1 - - - +
166B SER* 1.3 59.0 + - - +
167B VAL 3.3 2.9 - - - -
168B TYR* 3.2 7.0 + - - -
169B LEU* 2.8 27.1 + - - +
224B GLN* 3.7 2.0 - - - -
1008T PHE* 3.3 18.2 - - - -
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B THR 3.7 2.5 + - - -
163B LEU* 3.7 17.4 + - - +
164B LYS 3.7 0.6 - - - -
165B SER* 1.3 73.4 - - - +
167B VAL* 1.3 60.2 + - - +
170B SER* 2.8 32.9 + - - -
178B PHE* 3.6 38.2 - - - -
221B MET 4.8 0.3 + - - -
224B GLN* 3.2 33.9 + - - +
225B CYS* 3.9 4.5 + - - -
228B VAL* 3.6 7.0 - - - +
233B CYS* 5.5 0.2 - - - -
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B SER* 1.3 79.7 + - - +
168B TYR* 1.3 63.2 + - - +
170B SER* 3.4 2.5 + - - -
171B ARG* 3.2 54.5 + - - +
224B GLN* 2.9 49.1 + - - +
227B GLU* 3.6 37.5 - - + +
228B VAL* 3.7 9.9 - - + -
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Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 3.8 26.2 - - + -
110B ARG* 2.9 41.2 + - + -
111B GLN* 4.5 12.8 - - + +
134B ASP* 2.6 40.2 + - - -
137B MET* 3.5 15.4 - - + +
165B SER* 3.2 15.0 + - - +
167B VAL* 1.3 80.7 - - - +
169B LEU* 1.3 56.7 + - - +
171B ARG* 3.1 15.2 + - + +
172B LEU* 2.9 50.9 + - + +
224B GLN* 4.4 0.6 + - - -
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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
----------------------------------------------------------
72B PHE* 3.9 31.0 - - + -
103B ILE* 5.8 0.2 - - + -
107B LEU* 3.8 36.6 - - + -
141B ILE* 4.1 17.7 - - + -
162B THR* 3.4 34.1 - - - +
165B SER 2.8 19.8 + - - +
168B TYR* 1.3 73.5 - - - +
170B SER* 1.3 53.4 + - - +
172B LEU* 4.4 6.3 - - + -
173B PHE* 2.8 46.2 + - + +
176B SER* 3.7 0.5 + - - -
178B PHE* 3.6 22.9 - - + -
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B SER 2.8 19.0 + - - -
167B VAL 3.6 4.0 - - - -
169B LEU* 1.3 76.0 - - - +
171B ARG* 1.3 63.6 + - - +
173B PHE 3.2 16.1 - - - +
174B PRO* 3.4 8.7 - - - +
176B SER* 3.9 5.4 + - - -
178B PHE* 3.6 17.2 - - - -
228B VAL* 3.9 13.1 - - - +
232B LYS* 3.6 29.6 + - - +
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Residues in contact with ARG 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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138B GLN* 5.0 1.0 + - - -
167B VAL* 3.2 32.4 + - - +
168B TYR* 3.1 15.5 + - + +
170B SER* 1.3 76.5 - - - +
172B LEU* 1.3 66.5 + - + +
173B PHE 3.4 0.5 + - - -
174B PRO* 4.0 12.0 - - - +
227B GLU* 3.6 19.6 + - - -
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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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66B LYS* 4.0 2.8 - - - +
134B ASP* 3.6 39.9 - - + +
137B MET* 4.0 16.2 - - + -
138B GLN* 2.8 42.4 + - + +
141B ILE* 4.5 6.3 - - + -
168B TYR* 2.9 53.8 + - + +
169B LEU* 3.4 4.5 + - + +
171B ARG* 1.3 78.2 - - + +
173B PHE* 1.3 82.3 + - + +
174B PRO* 3.5 7.8 - - - +
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Residues in contact with PHE 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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65B GLY 5.0 0.2 - - - -
66B LYS* 3.5 20.6 - - - +
68B MET 5.3 0.9 - - - +
70B LEU* 3.8 15.9 - - + -
72B PHE* 3.9 18.6 - + - -
138B GLN* 3.9 27.8 - - + -
141B ILE* 4.1 24.7 - - + -
142B LEU* 3.5 35.0 - - + -
169B LEU* 2.8 26.1 + - + +
170B SER* 3.2 7.7 + - - +
172B LEU* 1.3 94.1 - - + +
174B PRO* 1.3 62.3 - - - +
175B ASN 3.2 2.9 - - - -
176B SER* 2.7 44.8 + - - +
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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
------------------------------------------------------------
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