Contacts of the helix formed by residues 111 - 120 (chain A) in PDB entry 4Z8J
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 THR 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A VAL 3.3 17.5 - - - +
60A SER* 3.8 7.6 - - - -
61A GLU* 3.7 28.0 + - + +
77A GLN* 3.6 0.9 - - - -
109A GLY 3.8 0.2 + - - -
110A ALA* 1.3 76.7 - - - +
112A HIS* 1.3 65.4 + - - +
113A LYS* 3.6 8.1 + - - +
114A GLN* 3.0 49.2 + - - +
115A VAL* 3.2 13.2 + - - +
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Residues in contact with HIS 112 (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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55A VAL* 3.2 33.6 - - + +
57A GLY 3.7 1.0 + - - +
58A GLN 3.0 25.5 + - - +
59A VAL* 3.9 7.3 + - + -
77A GLN* 2.8 27.6 + - - +
111A THR* 1.3 72.8 - - - +
113A LYS* 1.3 59.4 + - - +
115A VAL* 3.2 3.8 + - - +
116A VAL* 2.9 35.9 + - + +
589B TRP* 3.1 51.7 + + + -
591B THR* 2.7 27.8 + - - -
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Residues in contact with LYS 113 (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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59A VAL 5.2 0.8 + - - +
111A THR* 3.2 7.5 + - - +
112A HIS* 1.3 81.4 - - - +
114A GLN* 1.3 58.7 + - + +
116A VAL* 3.8 5.6 - - - -
117A ASP* 2.9 57.6 + - - +
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Residues in contact with GLN 114 (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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61A GLU* 3.5 11.3 + - - +
110A ALA* 3.4 15.8 - - + +
111A THR* 3.0 46.1 + - - +
113A LYS* 1.3 78.2 - - + +
115A VAL* 1.3 57.7 + - - +
117A ASP* 3.9 5.1 - - - +
118A LEU* 3.0 40.0 + - + +
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Residues in contact with VAL 115 (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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55A VAL* 4.2 18.2 - - + -
77A GLN* 3.6 27.6 - - + -
99A ILE* 4.6 5.6 - - + -
102A VAL* 4.2 11.7 - - + -
107A VAL* 3.7 33.0 - - + -
110A ALA* 3.9 5.2 - - + -
111A THR 3.2 7.6 + - - +
112A HIS 3.2 7.7 + - - +
114A GLN* 1.3 75.8 - - - +
116A VAL* 1.3 65.4 + - - +
118A LEU* 3.3 7.1 + - - +
119A ILE* 2.9 40.3 + - + +
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Residues in contact with VAL 116 (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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55A VAL* 4.1 11.4 - - + -
112A HIS* 2.9 46.3 + - + +
113A LYS* 3.8 5.4 - - - +
115A VAL* 1.3 74.8 - - + +
117A ASP* 1.3 66.8 + - - +
119A ILE* 3.2 9.6 + - - +
120A ARG* 3.0 62.5 + - - +
591B THR* 3.7 16.6 - - + +
593B MET* 4.2 5.8 - - + -
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Residues in contact with ASP 117 (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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113A LYS* 2.9 56.0 + - - +
114A GLN* 3.9 5.6 - - - +
116A VAL* 1.3 82.3 - - - +
118A LEU* 1.3 62.2 + - + +
120A ARG* 3.3 16.0 + - - +
121A ALA* 3.1 20.1 + - - +
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Residues in contact with LEU 118 (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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102A VAL* 3.6 20.9 - - + +
103A ASN* 2.9 26.2 + - + -
105A VAL* 3.9 39.3 - - + -
107A VAL* 3.6 29.2 - - + -
114A GLN* 3.0 26.7 + - + +
115A VAL 3.7 2.5 - - - +
116A VAL 3.3 0.2 - - - -
117A ASP* 1.3 75.0 - - + +
119A ILE* 1.3 66.0 + - - +
121A ALA* 3.1 17.3 + - + +
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Residues in contact with ILE 119 (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 TYR* 3.9 30.2 + - + -
53A PHE* 4.0 19.1 - - + -
55A VAL* 4.2 19.7 - - + -
99A ILE* 5.0 3.1 - - + -
102A VAL* 3.9 15.9 - - + -
103A ASN* 4.4 0.9 + - - -
115A VAL* 2.9 35.8 + - + +
116A VAL 3.2 6.3 + - - +
118A LEU* 1.3 76.2 - - - +
120A ARG* 1.3 60.5 + - + +
121A ALA 3.4 0.9 + - - -
122A GLY 4.3 3.8 + - - +
125A GLU 5.3 0.3 - - - +
126A LEU* 3.9 34.7 - - + +
128A LEU* 4.7 1.6 - - + -
593B MET* 3.5 24.2 - - + -
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Residues in contact with ARG 120 (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 TYR* 5.7 1.6 - - - -
116A VAL* 3.0 38.8 + - - +
117A ASP* 3.6 15.8 + - - +
118A LEU 3.2 0.2 - - - -
119A ILE* 1.3 75.7 - - + +
121A ALA* 1.3 61.3 + - - +
122A GLY 3.4 9.7 + - - +
591B THR* 3.7 24.5 - - - +
592B VAL 5.0 3.2 + - - -
593B MET* 4.0 15.3 - - + +
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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