Contacts of the helix formed by residues 91 - 102 (chain A) in PDB entry 1ZEB
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 ASP 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ASN* 3.2 6.1 - - - +
90A PRO* 1.3 74.7 - - - +
92A SEP 1.3 59.1 + - - +
93A GLY* 2.9 16.5 + - - -
94A ALA* 3.0 21.7 + - - +
95A THR* 2.7 36.8 + - - +
107A PHE* 3.4 22.0 - - + -
108A GLN* 2.9 41.1 + - + -
166A ARG* 3.2 16.2 + - - +
358A HIS* 4.3 4.5 - - - -
432A HIS* 3.9 7.6 - - + -
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Residues in contact with SEP 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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42A ASP* 3.2 4.5 + - - +
91A ASP* 1.3 73.2 - - - +
93A GLY* 1.3 61.5 + - - -
95A THR* 3.2 7.1 + - - -
96A ALA* 3.0 29.3 + - - +
99A TYR* 4.4 2.9 + - - -
153A HIS* 3.7 12.3 + - - -
154A ALA* 3.7 15.9 - - - +
155A SER* 3.9 9.6 + - - -
166A ARG* 2.8 39.7 + - - -
316A ASP* 2.7 6.9 + - - -
317A HIS* 5.4 0.2 + - - -
357A ASP* 3.4 7.0 - - - +
432A HIS* 2.8 15.1 + - - -
901A ZN 2.1 40.0 - - - -
902A ZN 2.1 53.3 - - - -
903A MG 4.3 0.2 - - - -
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Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASP* 2.9 12.7 + - - -
92A SEP 1.3 78.9 + - - -
94A ALA* 1.3 57.4 + - - +
96A ALA* 3.1 8.3 + - - +
97A THR* 3.1 26.5 + - - -
108A GLN 5.1 0.7 - - - -
109A THR 3.0 16.4 - - - +
110A ILE* 3.8 12.3 - - - -
154A ALA* 3.6 15.9 - - - +
166A ARG* 5.3 0.4 - - - -
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Residues in contact with ALA 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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84A ASN* 3.2 31.5 - - - +
91A ASP* 3.0 11.9 + - - +
93A GLY* 1.3 71.7 - - - +
95A THR* 1.3 63.2 + - - +
97A THR* 3.4 9.8 + - - -
98A ALA* 3.3 18.4 + - - +
104A LYS* 4.8 0.2 - - - -
105A GLY 3.6 15.3 + - - +
106A ASN 3.3 28.3 - - - +
109A THR* 3.1 5.6 + - - -
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Residues in contact with THR 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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82A THR 3.7 3.6 - - - +
84A ASN* 3.8 1.3 - - - +
90A PRO* 3.4 26.0 - - + -
91A ASP 2.7 25.5 + - - +
92A SEP 3.2 6.8 + - - -
94A ALA* 1.3 73.9 - - - +
96A ALA* 1.3 67.2 + - - +
98A ALA* 2.9 5.4 + - - +
99A TYR* 2.9 26.4 + - - -
357A ASP* 3.2 40.9 - - - +
358A HIS* 4.9 0.4 - - + -
455A GLN* 3.2 22.0 - - - +
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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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92A SEP 3.0 21.7 + - - +
93A GLY 3.1 6.3 + - - +
95A THR* 1.3 74.0 + - - +
97A THR* 1.3 57.6 + - - +
99A TYR* 3.4 22.6 - - + +
100A LEU* 2.8 39.3 + - + +
154A ALA 3.9 18.2 - - - +
155A SER 4.1 3.6 - - - +
158A GLY* 3.9 16.4 - - - -
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Residues in contact with THR 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 GLY 3.1 11.6 + - - -
94A ALA* 3.4 13.0 + - - -
96A ALA* 1.3 75.3 - - - +
98A ALA* 1.3 58.2 + - - +
101A CYS* 2.8 34.9 + - - +
102A GLY 3.0 7.4 + - - -
103A VAL* 3.1 16.0 - - + +
105A GLY* 4.6 3.8 - - - +
109A THR* 4.1 1.4 + - - -
110A ILE* 3.6 3.1 - - - -
111A GLY* 2.8 22.1 + - - +
112A LEU 3.5 25.8 + - - +
129A VAL* 3.6 23.8 - - + -
158A GLY* 5.2 0.4 - - - -
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Residues in contact with ALA 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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94A ALA 3.3 7.2 + - - +
95A THR* 2.9 10.1 + - - +
97A THR* 1.3 78.1 - - - +
99A TYR* 1.3 57.8 + - - +
102A GLY* 3.0 26.0 + - - -
103A VAL 3.1 16.3 + - - +
104A LYS* 4.2 10.8 - - + -
455A GLN* 3.7 19.3 - - + +
456A THR* 3.3 29.2 - - + +
459A ALA* 3.6 1.0 - - - +
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Residues in contact with TYR 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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38A ILE* 3.5 18.9 - - + +
40A LEU* 3.4 36.2 - - + +
92A SEP 4.4 0.5 + - - -
95A THR 2.9 35.9 + - - -
96A ALA* 3.4 17.7 - - - +
98A ALA* 1.3 72.7 - - - +
100A LEU* 1.3 86.5 + - + +
132A VAL* 5.0 0.5 - - - +
155A SER* 3.5 24.1 + - - -
309A PHE* 4.3 3.6 - + - -
355A THR* 5.0 0.7 - - + -
356A ALA 5.2 0.4 - - - -
357A ASP* 3.6 20.1 - - + +
455A GLN* 3.8 28.5 - - + -
458A ILE* 3.5 31.1 - - + +
459A ALA* 3.5 19.1 + - - +
462A MET* 5.1 1.9 - - - +
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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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38A ILE* 4.2 13.9 - - + -
96A ALA* 2.8 23.4 + - + +
99A TYR* 1.3 106.8 - - + +
101A CYS* 1.3 56.0 - - - +
102A GLY 3.7 0.4 - - - -
131A SER* 3.3 4.3 - - - -
132A VAL* 2.8 34.8 + - + +
133A MET 4.8 0.2 + - - -
155A SER 3.4 19.3 - - - +
158A GLY* 3.4 36.6 - - - +
159A THR* 3.5 14.6 - - + +
307A PHE* 4.5 9.4 - - + -
309A PHE* 4.1 15.9 - - + -
459A ALA* 3.8 2.5 - - - -
462A MET* 6.3 0.4 - - - -
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Residues in contact with CYS 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 THR* 2.8 25.6 + - - +
100A LEU* 1.3 71.3 - - - +
102A GLY* 1.3 62.1 + - - +
103A VAL* 3.4 7.6 + - - +
111A GLY* 4.2 7.2 - - - -
129A VAL* 3.5 43.1 - - + +
130A ILE 3.9 6.0 - - - +
131A SER* 3.7 12.6 - - - -
135A ARG* 3.1 23.7 + - - +
158A GLY 3.6 23.1 - - - -
162A HIS* 5.6 0.4 - - - -
459A ALA* 3.9 0.9 - - - -
460A HIS* 4.9 1.6 + - - -
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Residues in contact with GLY 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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97A THR 3.0 0.4 + - - -
98A ALA 3.0 17.1 + - - -
101A CYS* 1.3 74.3 - - - +
103A VAL* 1.3 68.1 + - - +
456A THR* 3.5 14.9 - - - +
459A ALA* 3.2 15.2 - - - +
460A HIS* 3.0 30.6 + - - -
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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