Contacts of the helix formed by residues 92 - 101 (chain A) in PDB entry 1BZH
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 CYS 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PRO* 3.9 8.3 - - - -
88A LEU 3.3 22.2 + - - -
89A PRO* 4.2 9.9 - - - +
90A ASN 3.6 1.8 - - - -
91A THR* 1.3 75.1 - - - +
93A GLY* 1.3 65.6 + - - +
95A PHE* 3.3 2.2 + - - +
96A TRP* 3.1 28.1 + - - -
122A ALA* 3.9 16.4 - - - -
123A GLN 4.7 2.2 - - - -
124A TYR* 3.6 32.5 - - + -
133A MET* 5.5 1.8 - - - -
135A PHE* 3.5 22.4 - - + -
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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
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90A ASN 5.2 1.0 - - - -
91A THR* 3.3 0.6 - - - +
92A CYS* 1.3 77.1 - - - +
94A HIS* 1.3 55.3 + - - +
96A TRP* 3.2 3.6 + - - +
97A GLU* 2.8 28.8 + - - +
135A PHE* 3.6 26.6 - - - -
137A ASP* 3.7 19.6 + - - -
138A THR* 3.4 13.4 + - - -
140A LEU* 4.0 0.5 - - - +
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Residues in contact with HIS 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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43A ARG* 3.4 41.9 + - + -
59A LEU* 3.3 27.7 - - + +
61A GLN* 4.0 22.8 + - - -
66A TYR 4.6 1.2 + - - -
67A ILE* 4.0 11.6 - - + -
90A ASN* 3.5 19.1 - - - -
91A THR* 3.5 25.3 - - + +
92A CYS 3.3 0.6 - - - -
93A GLY* 1.3 74.8 - - - +
95A PHE* 1.3 53.5 + - - +
97A GLU* 3.1 8.5 + - - -
98A MET* 2.7 32.6 + - - +
137A ASP* 3.6 17.7 + - - -
138A THR* 4.3 0.4 - - - -
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Residues in contact with PHE 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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67A ILE* 3.8 12.7 - - + +
84A THR* 3.8 19.3 - - + -
85A GLN 4.7 1.1 - - - -
87A PRO* 3.4 30.1 - - + -
91A THR 2.9 17.4 + - - +
92A CYS 3.5 4.5 - - - +
93A GLY 3.2 0.2 - - - -
94A HIS* 1.3 75.2 - - - +
96A TRP* 1.3 85.4 + + - +
98A MET* 2.9 10.6 + - + +
99A VAL* 2.8 37.8 + - + +
107A VAL* 3.7 25.4 - - + -
124A TYR* 3.5 27.1 - + - -
212A VAL* 3.7 23.8 - - + -
214A HIS* 4.3 4.7 - + - -
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Residues in contact with TRP 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 CYS* 3.1 22.9 + - - -
93A GLY 3.9 2.9 - - - +
95A PHE* 1.3 86.2 - + - +
97A GLU* 1.3 57.9 + - - +
99A VAL* 3.3 27.7 + - + +
100A TRP* 2.8 30.3 + - - +
107A VAL* 4.1 6.7 - - + -
124A TYR* 2.7 52.1 + + - +
125A TRP* 4.3 1.3 - - + -
135A PHE* 3.3 25.4 - + + -
140A LEU* 3.6 16.4 - - + +
142A LEU* 3.1 22.2 - - + +
158A LEU* 3.6 25.6 - - + -
160A LEU* 3.9 21.9 - - + +
171A ILE* 4.1 23.1 - - + -
173A HIS* 4.9 1.1 - + - -
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Residues in contact with GLU 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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59A LEU* 3.6 18.9 - - + +
61A GLN* 2.6 48.2 + - - +
93A GLY 2.8 11.0 + - - +
94A HIS* 3.4 4.8 - - - +
96A TRP* 1.3 72.5 - - - +
98A MET* 1.3 61.8 + - - +
100A TRP* 4.2 2.7 - - - -
101A GLU* 2.8 69.0 + - + +
138A THR* 3.1 32.6 + - + +
140A LEU* 3.5 6.9 - - - +
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Residues in contact with MET 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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57A ILE* 3.7 26.2 - - + -
59A LEU* 3.9 10.3 - - + +
67A ILE* 3.7 22.4 - - + -
69A ALA* 3.3 29.4 - - + -
82A ILE* 3.6 28.7 - - + -
84A THR* 3.9 16.8 - - + -
94A HIS 2.7 16.2 + - - +
95A PHE* 2.9 16.4 + - + +
97A GLU* 1.3 73.3 - - - +
99A VAL* 1.3 64.0 + - - +
101A GLU* 4.7 2.9 - - - -
102A GLN* 2.8 37.5 + - + +
212A VAL* 4.1 12.1 - - + -
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Residues in contact with VAL 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 PHE* 2.8 25.1 + - + +
96A TRP* 3.5 29.4 - - + +
98A MET* 1.3 79.3 - - + +
100A TRP* 1.3 62.9 + - - +
103A LYS* 3.3 1.2 + - - -
104A SER* 3.1 38.1 + - - +
107A VAL* 3.9 19.5 - - + -
160A LEU* 3.9 7.6 - - + -
169A ARG* 4.5 0.5 + - - -
171A ILE* 3.7 33.4 - - + -
212A VAL* 4.3 12.1 - - + -
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Residues in contact with TRP 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 TRP 2.8 17.1 + - - +
97A GLU* 3.5 8.1 - - - +
99A VAL* 1.3 79.7 - - - +
101A GLU* 1.3 75.7 + - + +
103A LYS* 3.3 4.0 + - - +
140A LEU* 4.3 13.0 - - + -
160A LEU* 3.3 44.4 - - + -
162A ASN* 3.4 35.0 - - + +
167A GLU* 3.4 52.2 - - + -
169A ARG* 2.5 65.0 + - + +
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Residues in contact with GLU 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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58A LYS 4.5 0.7 - - - +
59A LEU* 3.6 5.0 - - - -
60A HIS* 2.7 63.7 + - + +
97A GLU* 2.8 53.5 + - + +
98A MET* 4.2 2.3 + - - +
100A TRP* 1.3 85.6 - - + +
102A GLN* 1.3 68.8 + - - +
103A LYS* 3.4 11.3 + - - +
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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