Contacts of the helix formed by residues 92 - 106 (chain A) in PDB entry 2ZLB
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 ASN 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLU* 2.9 21.0 + - - +
91A MET* 1.3 72.0 - - - +
93A PRO* 1.4 69.7 - - - +
94A ASP* 3.0 33.2 + - - +
95A TYR* 3.2 42.0 + - + +
96A ALA* 3.1 21.8 + - - +
116A ASN* 3.9 0.2 - - - -
143A TRP* 5.0 4.3 - - + -
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Residues in contact with PRO 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 MET 3.2 9.1 - - - +
92A ASN* 1.4 84.7 - - - +
94A ASP* 1.3 67.1 + - - +
96A ALA* 3.7 1.7 - - - +
97A ALA* 3.0 28.2 + - - +
116A ASN* 3.4 25.4 - - - +
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Residues in contact with ASP 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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4A THR* 5.7 2.7 - - + -
6A GLU* 3.7 16.7 - - - +
92A ASN* 3.0 15.6 + - - +
93A PRO* 1.3 82.1 - - - +
95A TYR* 1.3 61.3 + - - +
97A ALA* 3.6 5.9 - - - +
98A ILE* 2.9 40.7 + - + +
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Residues in contact with TYR 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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6A GLU* 3.0 38.2 + - - +
67A ALA 3.3 26.9 - - - +
68A TYR* 3.3 46.6 + + - +
90A GLU* 3.7 4.0 - - + -
92A ASN* 3.2 33.7 + - + +
94A ASP* 1.3 74.3 - - - +
96A ALA* 1.3 58.2 + - - +
99A THR* 2.9 36.2 + - - -
142A HIS* 4.4 3.1 + - - -
143A TRP* 3.6 35.3 - + - -
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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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90A GLU* 3.9 15.8 - - + +
92A ASN 3.1 15.6 + - - +
93A PRO 3.7 5.2 - - - +
95A TYR* 1.3 75.9 - - - +
97A ALA* 1.3 56.7 + - - +
99A THR* 3.5 5.9 + - - -
100A GLN* 2.9 29.0 + - - +
114A ILE* 3.9 21.7 - - + +
116A ASN* 3.8 27.4 - - + -
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Residues in contact with ALA 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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10A LEU* 5.6 0.2 - - - -
93A PRO 3.0 18.0 + - - +
94A ASP* 3.6 8.7 - - - +
96A ALA* 1.3 74.5 - - - +
98A ILE* 1.3 60.4 + - + +
100A GLN* 3.4 7.7 + - - +
101A GLN* 2.9 35.7 + - + +
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Residues in contact with ILE 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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4A THR* 4.7 0.4 - - + -
6A GLU* 2.7 69.8 - - + +
7A GLN* 3.7 20.0 - - + +
10A LEU* 4.1 11.2 - - + +
68A TYR 4.3 2.2 - - - +
69A CYS* 3.9 22.7 - - - +
94A ASP* 2.9 23.5 + - + +
95A TYR* 3.9 3.4 - - - +
97A ALA* 1.3 73.0 - - + +
99A THR* 1.3 62.5 + - - +
101A GLN* 3.2 6.7 + - - +
102A MET* 2.9 36.7 + - + +
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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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67A ALA* 3.5 25.5 - - + +
68A TYR 3.8 2.6 + - - -
70A GLY* 3.3 34.3 + - - -
73A ALA* 4.0 19.5 - - + -
88A THR* 4.4 4.3 - - - +
95A TYR 2.9 20.5 + - - -
96A ALA* 3.7 5.2 - - - -
98A ILE* 1.3 76.4 - - - +
100A GLN* 1.3 63.1 + - - +
102A MET* 3.3 2.8 + - - +
103A LEU* 3.0 30.0 + - + +
114A ILE* 4.4 10.3 - - + -
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Residues in contact with GLN 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 2.9 17.3 + - - +
97A ALA* 3.5 7.6 - - - +
99A THR* 1.3 76.3 - - - +
101A GLN* 1.3 62.2 + - - +
103A LEU* 3.2 4.2 + - - +
104A ASN* 2.8 65.7 + - - +
109A GLN* 4.0 15.0 + - - +
112A VAL* 5.4 3.3 + - - +
114A ILE* 3.1 40.2 + - + +
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Residues in contact with GLN 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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10A LEU* 3.6 35.1 - - + +
14A GLN* 4.7 10.3 + - - +
97A ALA* 2.9 22.4 + - + +
98A ILE 3.2 0.8 + - - +
100A GLN* 1.3 81.8 - - - +
102A MET* 1.3 57.0 + - - +
104A ASN* 3.4 26.7 + - - +
105A PHE* 3.0 28.6 + - - +
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Residues in contact with MET 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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9A ILE* 3.8 22.0 - - + -
10A LEU* 3.8 24.7 - - + +
13A VAL* 3.7 31.9 - - + -
25A VAL* 4.0 7.9 - - + +
29A ILE* 3.6 26.5 - - + -
69A CYS 3.0 26.7 - - - +
70A GLY* 4.6 1.6 - - - -
74A VAL* 3.9 11.2 - - + +
98A ILE* 2.9 23.3 + - + +
99A THR* 3.5 5.6 - - - +
101A GLN* 1.3 75.3 - - - +
103A LEU* 1.3 64.0 + - - +
105A PHE* 3.5 5.1 + - - +
106A ALA* 3.1 24.6 + - - +
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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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73A ALA* 3.8 43.1 - - + +
74A VAL* 3.8 14.4 - - + +
77A ALA* 4.1 5.2 - - + -
99A THR* 3.0 22.7 + - + +
100A GLN* 3.2 6.3 + - - +
102A MET* 1.3 77.6 - - - +
104A ASN* 1.3 60.7 + - - +
106A ALA* 3.4 2.6 + - - +
107A GLY 3.2 3.6 + - - -
108A LEU* 2.9 34.6 + - + -
109A GLN* 4.2 12.1 - - - +
112A VAL* 3.6 42.4 - - + -
114A ILE* 3.7 14.8 - - + -
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Residues in contact with ASN 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 GLN* 2.8 34.2 + - - +
101A GLN* 3.5 33.7 + - - +
102A MET 3.3 0.2 - - - -
103A LEU* 1.3 72.2 - - - +
105A PHE* 1.3 59.9 + - - +
107A GLY* 2.8 24.9 + - - -
109A GLN* 3.0 37.3 + - - +
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Residues in contact with PHE 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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10A LEU* 6.0 0.9 - - + -
13A VAL* 3.8 13.2 - - + -
14A GLN* 3.7 47.6 - - + +
17A ALA* 3.5 32.5 - - + -
19A PRO* 3.3 44.8 - - + +
20A GLY 2.7 30.8 + - - -
25A VAL* 3.6 17.0 - - + -
101A GLN 3.0 13.8 + - - +
102A MET* 3.7 8.3 - - - +
104A ASN* 1.3 78.9 - - - +
106A ALA* 1.3 49.9 - - - +
107A GLY 3.1 1.4 + - - -
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Residues in contact with ALA 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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20A GLY* 3.4 20.1 - - - +
21A ASP 4.4 2.0 - - - +
22A PRO* 3.6 21.8 - - + +
25A VAL* 3.8 21.5 - - + +
74A VAL* 4.2 7.6 - - + -
102A MET 3.1 18.1 + - - +
103A LEU 3.8 5.4 - - - +
104A ASN 3.2 0.2 - - - -
105A PHE* 1.3 74.7 - - - +
107A GLY* 1.3 61.1 + - - +
108A LEU* 3.6 19.9 + - + +
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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