Contacts of the helix formed by residues 91 - 105 (chain A) in PDB entry 4Z1H
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 GLN 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A GLU 3.5 4.5 + - - +
90A PHE* 1.3 76.0 - - - +
92A ALA* 1.3 96.8 + - - +
93A GLU* 3.4 5.6 + - + +
94A THR* 3.2 16.8 - - + +
95A LYS* 3.0 22.2 + - - +
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Residues in contact with ALA 92 (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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90A PHE 3.9 0.2 + - - -
91A GLN* 1.3 94.5 + - - +
93A GLU* 1.3 59.6 + - - +
95A LYS* 4.0 3.2 - - - +
96A LYS* 2.9 45.5 + - - +
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Residues in contact with GLU 93 (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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91A GLN* 3.4 4.3 + - + +
92A ALA* 1.3 78.8 - - - +
94A THR* 1.3 64.4 + - - +
96A LYS* 3.4 12.0 + - - +
97A LEU* 3.3 39.0 + - + +
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Residues in contact with THR 94 (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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90A PHE* 3.7 23.6 - - + -
91A GLN* 3.2 36.9 - - + +
93A GLU* 1.3 77.3 - - - +
95A LYS* 1.3 63.8 + - - +
97A LEU* 3.4 16.8 - - - +
98A LEU* 2.9 29.2 + - - +
170A SER 5.8 1.3 + - - +
171A ASN 5.2 0.5 + - - -
206A TYR* 4.1 16.5 + - - -
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Residues in contact with LYS 95 (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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90A PHE* 3.8 15.7 - - + +
91A GLN 3.0 18.9 + - - +
92A ALA* 4.0 3.6 - - - +
94A THR* 1.3 75.3 - - - +
96A LYS* 1.3 66.8 + - + +
98A LEU* 3.2 11.5 - - + +
99A ASP* 2.6 63.7 + - - +
235A GLY 2.9 25.3 + - - -
236A SER* 3.7 13.4 + - - +
237A GLY* 4.0 17.3 - - - +
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Residues in contact with LYS 96 (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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92A ALA* 2.9 34.7 + - - +
93A GLU* 3.5 11.2 - - - +
95A LYS* 1.3 76.5 - - + +
97A LEU* 1.3 59.3 + - - +
99A ASP* 2.8 27.6 + - - +
100A ILE* 2.9 19.8 + - + +
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Residues in contact with LEU 97 (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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93A GLU* 3.4 38.8 - - + +
94A THR* 3.4 17.7 - - - +
96A LYS* 1.3 78.9 - - - +
98A LEU* 1.3 61.2 + - - +
100A ILE* 3.1 19.8 - - + +
101A VAL* 2.9 37.4 + - + +
203A VAL* 4.2 25.4 - - + -
206A TYR* 4.6 11.2 - - + -
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Residues in contact with LEU 98 (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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90A PHE* 3.8 36.3 - - + -
94A THR* 2.9 20.5 + - - +
95A LYS* 3.2 13.9 - - + +
96A LYS 3.0 0.2 + - - -
97A LEU* 1.3 81.8 - - - +
99A ASP* 1.3 60.9 + - - +
101A VAL* 3.7 2.3 - - - +
102A ALA* 2.9 30.1 + - + +
206A TYR* 3.5 26.9 - - + +
209A PHE* 3.4 37.0 - - + -
235A GLY* 4.1 11.2 - - - +
236A SER 3.9 10.8 - - - +
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Residues in contact with ASP 99 (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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95A LYS* 2.6 61.1 + - - +
96A LYS* 2.8 15.3 + - - +
98A LEU* 1.3 72.6 - - - +
100A ILE* 1.3 56.2 - - + +
102A ALA* 3.0 9.9 + - - +
103A ARG* 3.0 50.1 + - - +
235A GLY 4.3 1.9 - - - +
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Residues in contact with ILE 100 (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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96A LYS* 2.9 21.2 + - + +
97A LEU* 3.1 23.1 - - + +
98A LEU 3.3 0.2 - - - -
99A ASP* 1.3 76.8 - - + +
101A VAL* 1.3 65.8 + - + +
104A SER* 2.7 43.9 + - - +
105A LEU* 3.1 21.4 + - + -
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Residues in contact with VAL 101 (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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97A LEU* 2.9 23.6 + - + +
98A LEU 3.7 3.8 - - - +
100A ILE* 1.3 80.3 - - + +
102A ALA* 1.3 63.4 + - - +
103A ARG 3.2 1.0 + - - -
104A SER 4.2 1.2 + - - -
105A LEU* 3.5 29.0 + - + +
106A TYR* 4.0 16.6 - - + +
203A VAL* 4.0 25.6 - - + +
204A GLY 5.2 0.2 - - - +
206A TYR* 3.7 9.4 - - + -
207A SER* 3.5 34.1 - - - +
210A MET* 3.3 18.4 - - - +
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Residues in contact with ALA 102 (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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98A LEU* 2.9 19.4 + - + +
99A ASP* 3.0 12.3 + - - +
101A VAL* 1.3 78.2 - - - +
103A ARG* 1.3 78.0 + - + +
206A TYR 4.8 1.8 - - - +
209A PHE* 4.2 25.1 - - + +
210A MET* 3.5 29.6 - - - +
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Residues in contact with ARG 103 (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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99A ASP* 3.0 33.0 + - - +
101A VAL 3.2 0.6 + - - -
102A ALA* 1.3 99.0 - - + +
104A SER* 1.3 64.5 + - - +
106A TYR 5.7 2.2 - - - -
210A MET* 5.5 1.8 - - - -
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Residues in contact with SER 104 (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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100A ILE* 2.7 32.0 + - - +
101A VAL 4.2 0.4 + - - -
103A ARG* 1.3 76.0 - - - +
105A LEU* 1.3 62.0 + - - +
106A TYR 5.0 2.0 - - - -
210A MET* 5.8 0.2 - - - -
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Residues in contact with LEU 105 (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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100A ILE* 3.6 21.1 - - + +
101A VAL* 3.5 34.4 + - + -
104A SER* 1.3 82.2 - - - +
106A TYR* 1.3 93.4 + - + +
203A VAL* 5.6 3.4 - - + -
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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