Contacts of the helix formed by residues 112 - 121 (chain T) in PDB entry 2P8Z
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 112 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108T HIS* 2.7 40.1 + - - -
110T ASP* 2.9 16.2 - - - -
111T PHE 1.3 62.0 - - - -
113T SER* 1.3 61.1 + - - +
114T GLU* 3.5 5.1 + - - -
115T VAL* 3.1 11.3 + - - +
116T THR* 3.5 6.6 + - - -
145T GLN* 3.0 19.6 + - - -
483T PHE* 2.2 22.6 - - - -
484T SER 4.0 0.4 - - - -
485T VAL* 2.1 21.9 - - - +
517T CYS* 4.2 5.8 - - - -
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Residues in contact with SER 113 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111T PHE 3.9 0.6 + - - -
112T SER* 1.3 71.7 - - - +
114T GLU* 1.3 80.3 + - - +
115T VAL 3.2 0.9 - - - -
116T THR* 3.8 9.8 - - - -
117T ALA* 3.2 22.7 + - - +
465T LYS* 3.9 8.5 + - - -
480T VAL* 4.3 17.9 - - - +
485T VAL* 3.8 4.6 - - - +
517T CYS* 4.6 1.1 - - - -
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Residues in contact with GLU 114 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106T PRO* 4.0 10.5 - - + +
108T HIS* 3.1 30.3 - - + +
112T SER* 3.2 0.4 - - - +
113T SER* 1.3 82.0 + - - +
115T VAL* 1.3 61.8 + - - +
117T ALA* 3.5 7.1 + - - +
118T ALA* 3.3 19.8 + - - +
384T LYS* 5.9 3.7 - - + +
465T LYS* 3.0 12.0 + - - -
515T ASP* 5.6 0.2 - - - +
516T PRO* 2.7 37.0 - - + +
517T CYS* 1.9 54.5 + - + -
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Residues in contact with VAL 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105T SER* 5.5 4.7 - - - -
106T PRO* 4.1 22.0 - - + +
108T HIS* 3.2 16.8 - - + +
109T VAL* 4.9 0.4 - - + -
112T SER* 3.1 12.8 + - - +
114T GLU* 1.3 75.3 - - - +
116T THR* 1.3 66.2 + - - +
118T ALA* 3.0 4.5 + - - +
119T LEU* 3.0 42.1 + - + +
142T VAL* 4.4 11.2 - - + -
145T GLN* 3.9 7.2 - - - +
483T PHE* 3.0 39.9 - - + -
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Residues in contact with THR 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112T SER 3.5 4.6 + - - -
113T SER 3.9 7.6 - - - -
114T GLU 3.4 0.2 - - - -
115T VAL* 1.3 79.4 - - - +
117T ALA* 1.3 56.8 + - - +
119T LEU* 3.4 9.2 + - - +
120T ARG* 3.0 41.9 + - - +
145T GLN* 3.2 17.6 + - - +
149T GLU* 3.5 8.5 - - + +
480T VAL* 2.7 64.8 + - + +
481T MET 3.8 1.0 + - - -
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Residues in contact with ALA 117 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T SER 3.2 17.9 + - - +
114T GLU* 3.6 8.1 - - - +
115T VAL 3.1 0.6 - - - -
116T THR* 1.3 78.1 - - - +
118T ALA* 1.3 62.2 + - - +
120T ARG* 3.3 19.5 + - - +
121T VAL* 3.7 5.0 + - - +
381T TYR* 4.8 12.9 - - - +
383T SER* 3.0 40.0 + - - +
384T LYS* 5.6 2.7 - - + -
466T THR* 4.8 5.8 - - + -
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Residues in contact with ALA 118 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67S HIS* 5.4 2.7 - - + -
23T SER* 6.4 0.4 - - - -
103T ILE* 4.4 3.4 - - + +
104T ASP 3.9 21.5 - - - +
105T SER* 4.2 7.2 - - - -
106T PRO* 3.9 15.3 - - + -
114T GLU 3.3 9.2 + - - +
115T VAL 3.0 8.6 + - - +
117T ALA* 1.3 80.0 - - - +
119T LEU* 1.3 62.6 + - + +
121T VAL* 3.1 23.9 - - - +
122T THR* 3.5 8.9 - - - +
383T SER* 4.3 4.3 - - - -
384T LYS* 6.0 3.1 - - + +
397T PHE* 6.0 1.6 - - - -
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Residues in contact with LEU 119 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23T SER* 3.8 23.1 - - - +
25T ILE* 4.7 4.0 - - + -
105T SER* 5.2 7.0 - - - -
115T VAL* 3.0 39.5 + - + +
116T THR* 3.9 5.6 - - - +
118T ALA* 1.3 74.9 - - + +
120T ARG* 1.3 57.8 + - - +
122T THR* 2.6 38.7 + - - +
142T VAL* 4.1 15.0 - - + +
145T GLN* 4.0 11.4 - - + +
146T ALA* 3.8 31.0 - - + +
149T GLU* 4.3 5.6 - - + +
151T ILE* 3.6 25.8 - - + +
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Residues in contact with ARG 120 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116T THR* 3.0 23.1 + - - +
117T ALA* 3.3 10.5 - - - +
119T LEU* 1.3 77.3 - - - +
121T VAL* 1.3 56.9 + - + +
122T THR 3.3 0.6 + - - -
149T GLU* 2.7 36.8 + - - +
352T ARG* 2.8 32.5 + - - +
356T LEU* 4.0 25.8 - - + +
381T TYR* 3.8 35.1 + - + -
399T ARG* 4.1 0.3 + - - -
401T PHE* 4.5 4.2 - - + -
479T LYS* 1.2 57.9 + - - +
480T VAL* 2.1 43.0 - - - +
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Residues in contact with VAL 121 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T ASN* 3.8 3.6 - - - +
103T ILE* 3.7 33.9 - - + +
117T ALA 4.0 2.0 - - - +
118T ALA* 3.1 19.5 + - - +
120T ARG* 1.3 79.0 - - + +
122T THR* 1.3 58.7 + - - +
381T TYR* 4.9 8.1 - - + -
383T SER* 4.0 25.6 - - - +
397T PHE* 4.2 15.5 - - + -
398T GLY 4.9 0.4 - - - -
399T ARG* 3.5 43.6 + - + +
401T PHE* 5.7 0.9 - - + -
453T ILE* 3.8 14.1 - - + +
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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