Contacts of the strand formed by residues 3 - 12 (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 HIS 3 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G SER* 1.3 103.0 + - - +
4G SER* 1.3 61.9 + - - +
29G ASP* 2.7 31.9 + - - +
102G GLU* 3.1 7.0 - - - +
103G LEU* 2.6 40.6 + - + -
107G ARG* 3.6 25.3 + - - -
168G LEU* 4.2 7.9 - - + -
172G LEU* 3.5 26.1 - - + +
179G LEU 5.0 2.0 - - - -
180G LEU* 3.1 36.1 - - + +
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Residues in contact with SER 4 (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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3G HIS* 1.3 81.4 - - - +
5G LEU* 1.3 61.9 + - - +
6G LYS* 3.7 25.4 - - - -
27G TYR 3.7 0.4 - - - +
28G VAL* 3.3 5.9 - - - +
29G ASP* 2.9 42.7 + - - -
101G CYS 3.3 11.9 - - - -
102G GLU* 3.7 16.4 - - - -
168G LEU* 3.9 10.2 - - - +
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Residues in contact with LEU 5 (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* 1.3 75.4 - - - +
6G LYS* 1.3 66.3 + - - +
7G TYR* 3.6 21.7 - - + -
27G TYR 3.4 12.1 - - - +
28G VAL* 4.6 2.2 - - + +
33G PHE* 3.6 20.6 - - + -
99G HIS* 5.4 0.2 + - - -
100G GLY* 3.1 2.4 - - - -
101G CYS* 3.0 32.0 + - - -
164G CYS* 3.6 33.3 - - - +
167G TRP* 4.6 0.2 - - + -
168G LEU* 4.1 18.6 - - + +
171G TYR* 3.9 24.0 - - + -
1S VAL 4.2 15.9 - - - +
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Residues in contact with LYS 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G SER* 3.7 18.8 + - - -
5G LEU* 1.3 78.3 - - - +
7G TYR* 1.3 69.1 + - - +
8G PHE* 4.1 30.0 - - + -
25G VAL 3.8 0.5 - - - +
26G GLY* 3.5 1.4 - - - -
27G TYR* 3.0 37.8 + - + +
29G ASP 3.6 22.4 + - - +
30G ASP* 5.4 1.6 + - - -
98G MET* 6.3 0.2 - - + -
99G HIS 3.2 15.7 - - - +
100G GLY* 3.7 3.6 - - - -
113G TYR* 3.4 29.8 - - + +
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Residues in contact with TYR 7 (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* 3.6 19.3 - - + -
6G LYS* 1.3 79.1 - - - +
8G PHE* 1.3 67.8 + - - +
9G HIS* 3.3 28.0 - + + +
24G SER* 5.5 0.7 - - - -
25G VAL 3.2 7.2 - - - -
26G GLY* 4.0 7.9 - - - -
33G PHE* 3.5 19.4 - + - -
34G VAL* 4.1 18.3 - - + +
45G MET* 4.8 6.1 - - + -
59G TYR* 4.6 0.2 + - - -
63G GLU* 3.6 6.6 + - - -
98G MET* 3.5 22.3 - - - +
99G HIS* 3.0 30.8 + + + +
159G TYR* 3.9 2.5 - - - -
171G TYR* 3.9 0.9 + - - -
1S VAL* 2.9 46.9 + - - -
2S MET* 3.3 21.1 - - + -
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Residues in contact with PHE 8 (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* 4.1 39.9 - - + -
7G TYR* 1.3 79.5 - - - +
9G HIS* 1.3 61.8 + - - +
10G THR* 4.1 1.4 + - - -
23G ILE 3.6 1.7 - - - +
24G SER* 3.3 4.3 - - - -
25G VAL* 2.8 45.8 + - + +
27G TYR* 4.0 22.2 - + + -
97G TRP 3.9 2.7 - - - -
98G MET* 4.0 22.9 - - + -
54H LEU 5.3 1.2 - - - +
55H SER* 4.0 11.2 - - - +
56H PHE* 3.4 58.2 - + + -
57H SER* 5.0 4.0 - - - -
63H TYR* 5.5 1.6 - - - -
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Residues in contact with HIS 9 (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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7G TYR* 3.3 33.7 - + + +
8G PHE* 1.3 70.2 - - - +
10G THR* 1.3 63.4 + - - +
22G PHE* 4.0 19.4 - + + -
23G ILE 3.3 3.1 - - - -
24G SER* 2.8 32.3 + - - -
74G PHE* 4.5 3.2 - - + -
95G LEU 3.9 1.1 - - - +
96G GLN* 3.3 5.9 - - - -
97G TRP* 2.9 81.6 + + + +
99G HIS* 3.3 15.4 + + - -
56H PHE* 3.9 2.0 - - - -
2S MET* 3.7 24.3 - - + -
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Residues in contact with THR 10 (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 4.8 1.0 + - - -
9G HIS* 1.3 72.9 - - - +
11G SER* 1.3 63.0 + - - +
12G VAL* 4.0 19.1 - - + -
21G ARG 3.9 0.7 - - - +
22G PHE* 3.3 6.5 - - - -
23G ILE* 2.8 43.7 + - - +
94G THR* 4.0 7.6 - - + -
95G LEU 3.7 1.8 - - - -
96G GLN* 3.9 1.7 - - + +
54H LEU* 4.4 15.8 + - + +
56H PHE* 3.1 31.2 - - - -
62H PHE* 3.4 30.1 - - + -
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Residues in contact with SER 11 (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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10G THR* 1.3 75.3 - - - +
12G VAL* 1.3 60.7 + - - +
13G SER 4.2 0.2 - - - -
20G PRO* 4.3 4.9 - - - +
21G ARG 3.2 13.1 + - - -
22G PHE* 4.1 7.0 - - - +
71G ALA 5.2 0.7 + - - -
74G PHE* 3.8 33.0 - - - +
75G ARG 4.8 0.2 + - - -
78G LEU* 3.5 21.6 - - - +
93G HIS 3.7 0.9 - - - +
94G THR* 3.5 4.0 - - - +
95G LEU* 2.9 40.6 + - - +
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Residues in contact with VAL 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G THR* 4.0 15.9 - - + -
11G SER* 1.3 77.6 - - - +
13G SER* 1.3 64.8 + - - +
14G ARG* 3.5 8.1 + - + -
20G PRO* 3.4 3.3 - - - +
21G ARG* 2.9 41.4 + - + -
92G SER* 3.4 23.1 - - - +
93G HIS 3.3 7.2 - - - +
94G THR* 4.1 9.6 - - - +
32H PRO* 6.2 1.3 - - + -
33H SER* 3.1 31.0 - - - +
34H ASP* 5.2 9.4 - - - +
54H LEU* 6.1 0.4 - - + -
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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