Contacts of the strand formed by residues 94 - 103 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10G THR* 4.0 12.6 - - + -
11G SER 3.5 8.3 - - - +
12G VAL* 4.1 5.7 - - + +
78G LEU* 4.5 0.4 - - - -
93G HIS* 1.3 77.4 + - - +
95G LEU* 1.3 63.5 + - - +
96G GLN* 3.8 31.4 - - + +
117G ALA 3.6 0.5 - - - +
118G TYR* 3.2 10.1 - - - -
119G ASP* 2.7 37.9 + - - -
120G GLY 4.6 0.2 + - - -
31H HIS* 3.9 24.2 - - + -
32H PRO* 4.3 7.8 - - - +
33H SER* 4.0 11.3 + - - -
62H PHE* 4.2 3.8 - - + -
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Residues in contact with LEU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G HIS 3.9 0.9 - - - +
10G THR* 3.7 1.9 - - - -
11G SER* 2.9 36.5 + - - +
74G PHE* 3.7 35.7 - - + +
77G ASN* 3.4 37.0 - - + +
78G LEU* 3.9 19.0 - - + +
81G LEU* 4.3 9.9 - - + -
94G THR* 1.3 73.0 - - - +
96G GLN* 1.3 69.7 - - - +
116G PHE* 4.3 9.6 - - + -
117G ALA 3.3 17.0 - - - +
118G TYR* 4.6 2.5 - - + -
123G TYR* 6.0 0.7 - - + -
9S LEU* 4.0 18.8 - - + -
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Residues in contact with GLN 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G HIS 3.3 4.0 - - - +
10G THR* 3.9 15.5 - - + +
74G PHE* 4.8 0.2 - - - -
94G THR* 3.8 10.5 - - + +
95G LEU* 1.3 81.3 - - - +
97G TRP* 1.3 63.0 + - - +
116G PHE* 3.1 7.1 - - - +
117G ALA* 2.8 33.8 + - + +
120G GLY* 4.2 5.9 + - - -
31H HIS* 3.0 22.2 + - - -
56H PHE* 3.2 31.5 - - + -
60H TRP* 3.0 49.4 + - + +
62H PHE* 3.5 13.7 - - - -
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Residues in contact with TRP 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G PHE* 3.9 0.2 - - - -
9G HIS* 2.9 65.0 + + + +
70G THR* 3.8 18.6 - - + -
74G PHE* 3.4 29.2 - + + -
96G GLN* 1.3 77.4 - - - +
98G MET* 1.3 66.4 + - - +
99G HIS* 3.9 13.2 - + - -
114G GLU* 3.3 31.2 + - - +
115G GLN 3.2 16.6 - - - -
116G PHE* 3.4 25.3 - + + -
156G GLN* 4.1 4.3 - - - -
56H PHE* 4.0 1.8 - - - -
2S MET* 5.0 0.2 - - + -
3S ALA* 3.9 14.4 - - + -
5S ARG 3.4 17.9 - - - -
6S THR* 3.2 37.2 - - - -
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Residues in contact with MET 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LYS* 6.3 0.2 - - + -
7G TYR 3.5 12.3 - - - +
8G PHE* 4.0 21.5 - - + -
97G TRP* 1.3 76.4 - - - +
99G HIS* 1.3 64.7 + - - +
113G TYR* 5.3 12.6 - - + -
114G GLU* 3.4 2.3 - - - +
115G GLN* 2.8 53.3 + - + +
56H PHE* 3.4 15.0 - - + -
57H SER 3.9 13.0 - - - +
58H LYS* 3.9 25.6 - - - +
60H TRP* 3.2 38.1 - - + -
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Residues in contact with HIS 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LYS* 3.2 5.0 - - - +
7G TYR* 3.0 57.3 + + + -
9G HIS* 3.3 25.6 + + - -
97G TRP* 3.9 26.2 - + - -
98G MET* 1.3 77.4 - - - +
100G GLY* 1.3 60.1 + - - +
113G TYR* 3.2 16.2 - - - +
114G GLU* 3.8 18.4 - - + +
159G TYR* 3.5 25.4 + + - -
160G LEU* 4.5 4.3 - - + -
3S ALA* 3.5 20.4 + - + +
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Residues in contact with GLY 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G LEU 3.1 13.0 - - - -
6G LYS* 3.7 3.8 - - - -
99G HIS* 1.3 78.4 + - - +
101G CYS* 1.3 62.2 + - - -
112G GLY* 3.3 2.3 - - - -
113G TYR* 2.9 52.4 + - - +
160G LEU* 3.7 7.0 - - - +
164G CYS* 4.4 1.3 - - - -
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Residues in contact with CYS 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G SER* 3.3 3.9 - - - -
5G LEU* 3.0 36.9 + - - -
100G GLY* 1.3 75.0 - - - +
102G GLU* 1.3 62.2 + - - +
109G PHE* 4.3 4.3 - - + -
111G ARG 3.4 8.3 - - - +
113G TYR* 4.8 0.4 + - - -
160G LEU* 3.5 20.2 - - - +
164G CYS* 2.0 60.1 - - - -
165G VAL* 3.7 8.7 - - + -
168G LEU* 4.2 5.4 - - - +
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Residues in contact with GLU 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G SER* 5.4 4.5 + - - +
3G HIS 3.1 6.7 - - - +
4G SER* 3.7 18.6 - - - -
101G CYS* 1.3 78.3 - - - +
103G LEU* 1.3 65.6 + - - +
109G PHE* 3.9 5.2 - - - -
110G LEU* 2.9 29.5 + - + +
111G ARG* 2.2 61.5 + - - +
113G TYR* 2.9 33.7 + - + +
165G VAL* 6.1 0.4 - - - -
58H LYS* 5.3 4.7 + - - -
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Residues in contact with LEU 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G SER* 3.2 12.1 + - - -
3G HIS* 2.6 35.8 + - + +
102G GLU* 1.3 75.4 - - - +
104G GLY* 1.3 65.7 + - - +
107G ARG* 3.3 21.8 - - - +
108G ARG 3.1 26.9 - - - +
109G PHE* 3.6 5.4 - - - +
110G LEU* 4.0 2.8 - - - +
165G VAL* 3.8 19.7 - - + -
168G LEU* 3.4 33.4 - - + -
169G HIS* 3.3 32.3 - - + +
172G LEU* 4.6 5.4 - - + -
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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