Contacts of the helix formed by residues 92 - 109 (chain A) in PDB entry 4ZSL
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 VAL 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ASN 5.0 0.6 + - - -
89A ALA 5.1 0.2 + - - -
90A PHE 3.5 0.6 - - - -
91A ASP* 1.3 90.0 - - + +
93A VAL* 1.4 65.7 + - - +
94A THR* 3.8 25.4 - - + +
95A ASN* 3.2 20.3 + - + +
96A ALA* 3.0 22.5 + - - +
374A ARG* 4.0 4.3 - - - +
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Residues in contact with VAL 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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92A VAL* 1.4 71.2 - - - +
94A THR* 1.4 56.9 + - - +
96A ALA* 3.2 2.6 + - - +
97A LYS* 2.9 48.8 + - + +
372A LEU 4.3 9.9 - - - +
373A THR* 4.8 1.8 - - - -
374A ARG* 3.5 37.7 - - + +
377A ILE* 4.0 11.1 - - + +
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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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92A VAL* 3.8 17.9 - - + +
93A VAL* 1.4 79.6 - - - +
95A ASN* 1.3 71.3 + - - +
97A LYS* 3.8 7.8 - - - +
98A ARG* 3.2 22.2 + - - +
101A ARG* 5.3 1.0 + - - -
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Residues in contact with ASN 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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86A ILE* 5.9 0.7 - - - +
88A ASN 5.8 1.8 - - - +
89A ALA* 4.3 7.4 - - - +
92A VAL* 3.2 29.8 + - + +
94A THR* 1.3 83.2 - - - +
96A ALA* 1.3 61.1 + - - +
98A ARG* 3.3 3.1 + - - +
99A THR* 3.0 16.8 + - - -
401A 4QZ 2.9 41.8 + - - +
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Residues in contact with ALA 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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89A ALA 3.4 21.0 + - - +
90A PHE* 4.3 12.3 - - + +
92A VAL 3.0 16.8 + - - +
93A VAL* 3.7 4.7 - - - +
95A ASN* 1.3 76.0 - - - +
97A LYS* 1.4 61.2 + - - +
99A THR* 3.2 3.6 + - - -
100A LEU 3.1 17.7 + - - -
374A ARG* 5.2 3.1 - - - +
377A ILE* 3.4 31.9 - - + +
381A ILE* 3.5 8.2 - - + +
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Residues in contact with LYS 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 VAL* 2.9 37.8 + - + +
94A THR* 3.8 8.1 - - - +
96A ALA* 1.4 71.3 - - - +
98A ARG* 1.3 57.1 + - - +
100A LEU* 3.4 6.6 + - + +
101A ARG* 3.0 43.9 + - - +
367A PHE* 4.6 2.5 + - - -
368A ASP* 2.9 43.8 + - - +
370A GLU 3.0 20.4 + - - -
371A ALA* 5.2 0.6 - - - +
372A LEU* 4.8 7.4 - - - +
377A ILE* 3.7 22.2 - - + +
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Residues in contact with ARG 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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65A ALA 5.1 0.4 + - - -
66A TYR* 4.2 7.3 - - - -
94A THR 3.2 12.0 + - - +
95A ASN* 3.5 9.6 - - - +
96A ALA 3.3 0.2 - - - -
97A LYS* 1.3 76.4 - - - +
99A THR* 1.3 63.8 + - - +
101A ARG* 3.4 26.2 + - - +
102A GLU* 2.7 57.7 + - - +
200A ASP* 2.8 30.3 + - - +
202A GLY* 3.4 22.6 - - - +
401A 4QZ 3.4 59.2 + - - +
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Residues in contact with THR 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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86A ILE* 3.9 32.6 - - + +
89A ALA* 4.7 9.2 + - + -
95A ASN 3.0 7.9 + - - -
96A ALA* 3.6 9.3 - - - -
98A ARG* 1.3 76.1 - - - +
100A LEU* 1.4 57.3 + - - +
102A GLU* 3.4 1.9 + - - +
103A LEU* 3.0 41.9 + - + +
133A VAL* 5.0 2.7 - - + -
381A ILE* 4.0 19.1 - - + -
401A 4QZ 2.9 35.6 + - + -
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Residues in contact with LEU 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 ALA 3.1 13.3 + - - +
97A LYS* 3.7 10.5 - - + +
99A THR* 1.4 76.2 - - - +
101A ARG* 1.4 61.3 + - - +
103A LEU* 3.4 3.9 + - + +
104A LYS* 3.1 36.8 + - + +
367A PHE* 4.0 27.4 - - + +
372A LEU* 4.8 12.6 - - + -
377A ILE* 4.3 11.7 - - + -
380A ALA* 3.8 36.6 - - + +
381A ILE* 3.9 14.0 - - + +
384A GLU* 3.8 27.4 - - + +
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Residues in contact with ARG 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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94A THR 5.3 1.0 + - - -
97A LYS* 3.0 33.8 + - - +
98A ARG* 3.4 26.7 + - - +
100A LEU* 1.4 75.6 - - - +
102A GLU* 1.3 58.8 + - - +
104A LYS* 3.8 1.4 - - - +
105A ILE* 3.0 49.3 + - + +
201A PHE 3.9 6.5 - - - +
202A GLY* 2.9 25.0 + - - -
204A ALA 3.6 20.9 - - - -
205A ARG* 3.6 21.4 - - - +
363A PHE* 4.7 0.2 - - - -
365A PHE* 4.0 10.8 - - + -
367A PHE* 3.9 17.2 - - + -
368A ASP* 2.8 35.3 + - - +
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Residues in contact with GLU 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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66A TYR* 2.7 33.7 + - - -
98A ARG* 2.7 50.0 + - - +
101A ARG* 1.3 78.1 - - - +
103A LEU* 1.4 55.7 + - - +
105A ILE* 3.9 6.4 - - - +
106A LEU* 3.0 43.0 + - + +
201A PHE* 2.8 33.8 + - + +
202A GLY 3.9 0.4 + - - -
401A 4QZ 3.6 30.9 - - + -
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Residues in contact with LEU 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 THR* 3.0 27.6 + - + +
100A LEU* 3.9 3.6 - - - +
102A GLU* 1.4 74.5 - - - +
104A LYS* 1.3 57.2 + - - +
107A LYS* 3.0 39.1 + - + +
117A ILE* 3.9 8.1 - - + +
120A ILE* 3.8 26.7 - - + -
133A VAL* 5.2 2.9 - - + -
135A VAL* 4.2 14.4 - - + -
381A ILE* 3.8 34.5 - - + +
384A GLU* 4.5 21.1 - - + -
385A ILE* 4.9 5.6 - - + -
401A 4QZ 3.5 24.2 - - + -
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Residues in contact with LYS 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 LEU* 3.1 25.3 + - + +
101A ARG 3.8 3.6 - - - +
103A LEU* 1.3 73.0 - - - +
105A ILE* 1.3 65.0 + - - +
107A LYS* 3.5 3.7 + - - +
108A HIS* 3.0 24.6 + - - +
363A PHE* 3.6 19.2 - - + -
364A ASP 5.8 0.2 + - - -
367A PHE* 3.6 46.1 - - + -
384A GLU* 3.3 41.0 + - + +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ARG* 3.0 40.3 + - + +
102A GLU* 3.9 3.8 - - - +
104A LYS* 1.3 73.7 - - - +
106A LEU* 1.3 63.1 + - + +
108A HIS* 3.1 5.2 + - - +
109A PHE* 3.1 50.6 + - + -
178A VAL* 4.8 3.1 - - + -
201A PHE* 3.6 29.4 - - + +
204A ALA* 3.7 28.5 - - + -
363A PHE* 3.7 28.0 - - + -
365A PHE* 3.7 9.2 - - + -
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Residues in contact with LEU 106 (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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66A TYR* 3.8 17.9 - - - +
102A GLU* 3.0 24.5 + - + +
105A ILE* 1.3 76.1 - - + +
107A LYS* 1.3 56.7 + - - +
109A PHE* 3.2 23.2 - - - +
114A ILE* 4.4 4.0 - - + -
115A ILE* 3.4 35.1 - - + +
116A ALA* 5.1 1.2 - - - -
117A ILE* 3.7 28.4 + - + +
137A LEU* 4.5 7.0 - - + -
201A PHE* 3.6 36.1 - - + -
401A 4QZ 3.8 22.7 - - + -
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Residues in contact with LYS 107 (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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103A LEU 3.0 25.3 + - - +
104A LYS* 3.8 4.9 - - - +
105A ILE 3.3 0.2 - - - -
106A LEU* 1.3 75.8 - - - +
108A HIS* 1.4 64.1 + - - +
109A PHE 3.9 3.6 - - - +
110A LYS* 6.0 0.2 - - - +
117A ILE* 4.2 11.9 - - + -
120A ILE* 4.8 5.8 - - + -
384A GLU* 2.7 58.7 + - + +
387A ASP* 2.8 30.4 + - - +
388A PHE* 3.6 28.7 - - + +
391A ARG* 5.5 2.0 - - - +
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Residues in contact with HIS 108 (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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104A LYS 3.0 13.8 + - - +
105A ILE 3.1 9.4 + - - +
107A LYS* 1.4 77.9 - - - +
109A PHE* 1.3 72.6 + + + +
176A ALA* 4.6 0.2 - - + -
359A CYS* 3.6 19.4 - - - -
361A PRO* 2.9 37.1 + - + -
362A PRO 3.9 11.7 - - - -
363A PHE* 3.6 31.3 + + + -
404A GOL 3.0 44.5 + - - -
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Residues in contact with PHE 109 (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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105A ILE* 3.1 37.8 + - + +
106A LEU* 3.2 18.4 - - - +
107A LYS 3.4 3.9 - - - +
108A HIS* 1.3 92.9 - + - +
110A LYS* 1.3 60.7 + - - +
111A HIS 4.0 0.2 - - - -
114A ILE* 3.8 33.4 - - + -
115A ILE 5.8 0.4 - - - +
116A ALA* 5.9 3.3 - - - +
172A TYR* 3.5 23.1 - + + -
173A MET* 3.8 30.5 - - + -
176A ALA* 3.6 24.9 - - + -
178A VAL* 3.8 24.7 - - + -
201A PHE* 3.9 6.5 - + - -
359A CYS* 4.0 2.2 - - - -
363A PHE* 5.4 0.7 - + + -
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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