Contacts of the strand formed by residues 94 - 103 (chain C) in PDB entry 3BZE
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 THR 94 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C THR* 4.0 6.7 - - + -
11C SER 3.5 7.4 - - - +
12C VAL* 4.1 12.4 - - + +
78C LEU* 4.4 0.4 - - - -
93C HIS* 1.3 76.4 + - - +
95C LEU* 1.3 61.5 + - - +
96C GLN* 3.9 30.9 - - + +
117C ALA 3.7 0.3 - - - +
118C TYR* 3.2 9.9 - - - -
119C ASP* 2.5 40.5 + - - -
31D HIS* 3.9 19.7 - - + -
32D PRO* 4.1 15.4 - - - +
33D SER* 5.0 0.5 + - - -
62D PHE* 4.0 15.3 - - + -
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C HIS 3.9 0.3 - - - +
10C THR* 3.7 1.6 - - - -
11C SER* 3.0 34.2 + - - +
74C PHE* 3.6 37.4 - - + +
77C ASN* 3.5 35.4 - - + +
78C LEU* 3.8 16.8 - - + +
81C LEU* 4.2 13.9 - - + -
94C THR* 1.3 73.1 - - - +
96C GLN* 1.3 68.9 + - - +
116C PHE* 4.3 10.3 - - + -
117C ALA 3.4 16.8 - - - +
118C TYR* 5.3 0.2 - - + -
123C TYR* 6.1 1.1 - - + -
9Q LEU* 4.1 17.9 - - + -
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Residues in contact with GLN 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C HIS 3.2 3.1 - - - +
10C THR* 3.8 15.5 - - - +
74C PHE* 4.7 0.2 - - - -
94C THR* 3.9 10.1 - - + +
95C LEU* 1.3 80.4 - - - +
97C TRP* 1.3 62.3 + - - +
116C PHE* 3.2 7.1 - - - +
117C ALA* 2.8 33.7 + - + +
120C GLY* 4.1 5.0 + - - -
31D HIS* 2.8 25.1 + - - -
56D PHE* 3.2 30.3 - - + -
60D TRP* 2.9 48.6 + - + +
62D PHE* 3.2 16.1 - - - -
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Residues in contact with TRP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PHE* 3.6 0.7 - - - -
9C HIS* 2.7 73.5 + + + +
70C THR* 3.8 16.4 - - + -
74C PHE* 3.5 31.4 - + + -
96C GLN* 1.3 77.1 - - - +
98C MET* 1.3 73.4 + - - +
99C HIS* 3.9 14.8 - + - -
114C GLU* 3.4 29.2 + - - +
115C GLN 3.3 15.0 - - - -
116C PHE* 3.3 30.1 - + + -
156C GLN* 4.1 8.1 - - - -
56D PHE* 3.8 2.1 - - - -
60D TRP* 4.2 0.9 - - - -
2Q MET* 4.6 2.0 - - + -
3Q ALA* 3.7 21.5 - - + -
5Q ARG 3.8 2.2 - - - -
6Q THR* 3.5 32.8 - - - -
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Residues in contact with MET 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C TYR 3.3 16.2 - - - +
8C PHE* 3.5 21.3 - - + -
9C HIS* 4.7 0.4 - - - -
97C TRP* 1.3 77.5 - - - +
99C HIS* 1.3 63.3 + - - +
113C TYR* 4.5 13.2 - - + -
114C GLU* 2.9 24.6 - - - +
115C GLN* 2.9 27.6 + - + +
56D PHE* 3.8 14.1 - - + -
57D SER 4.2 4.5 - - - +
58D LYS* 3.7 22.2 - - - +
60D TRP* 3.1 50.5 - - + -
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Residues in contact with HIS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LYS* 2.6 34.6 - - - +
7C TYR* 3.1 41.1 + + + -
9C HIS* 3.0 31.3 + + - -
97C TRP* 3.9 21.3 - + - -
98C MET* 1.3 76.0 - - - +
100C GLY* 1.3 54.1 + - - +
113C TYR* 3.6 12.6 - - - +
114C GLU* 3.6 24.2 - - + +
159C TYR* 3.2 27.3 + + - -
160C LEU* 3.7 6.1 - - + -
3Q ALA* 3.7 15.8 + - + -
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Residues in contact with GLY 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU 3.7 2.7 - - - -
6C LYS* 3.4 17.5 - - - -
99C HIS* 1.3 80.8 + - - +
101C CYS* 1.3 61.5 + - - +
112C GLY* 3.1 24.1 - - - -
113C TYR* 3.3 22.5 + - - +
160C LEU* 4.0 8.7 - - - +
164C CYS* 4.0 5.4 - - - -
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Residues in contact with CYS 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C SER* 3.3 3.2 - - - -
5C LEU* 3.1 45.2 + - - -
6C LYS* 4.8 0.4 - - - +
100C GLY* 1.3 71.4 - - - -
102C GLU* 1.3 63.0 + - - +
109C PHE* 6.2 0.2 - - + -
111C ARG 3.7 7.6 - - - +
113C TYR* 4.6 0.6 - - - -
160C LEU 3.3 16.8 - - - +
164C CYS* 2.0 46.7 - - - -
165C VAL* 3.4 23.6 - - + -
168C LEU* 3.5 7.9 - - + +
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Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER* 5.1 6.8 + - - +
3C HIS 3.2 5.8 - - - +
4C SER* 3.8 20.0 - - - -
6C LYS* 6.1 0.3 - - - +
101C CYS* 1.3 75.0 - - - +
103C LEU* 1.3 62.7 + - - +
108C ARG 3.2 1.7 - - - +
109C PHE* 4.1 1.4 - - - -
110C LEU* 3.1 43.7 + - + +
111C ARG* 3.1 25.6 + - + +
113C TYR* 4.1 23.6 - - + +
165C VAL* 5.5 0.2 - - - +
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C SER* 2.6 38.8 + - - -
3C HIS* 2.5 16.8 + - + +
102C GLU* 1.3 74.8 - - - +
104C GLY* 1.3 55.8 + - - +
107C ARG* 2.7 49.1 - - + +
108C ARG 3.4 7.2 - - - +
110C LEU* 3.8 2.4 - - - +
165C VAL* 3.5 32.8 - - + +
168C LEU* 3.3 33.7 - - + -
169C HIS* 5.2 7.4 - - + +
172C LEU* 4.3 14.6 - - + -
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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