Contacts of the strand formed by residues 68 - 74 (chain B) in PDB entry 3C6M
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 LEU 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A SER* 4.0 21.3 - - - +
116A ARG 4.1 8.1 - - - +
117A GLY* 3.8 25.4 - - - +
11B PHE 3.5 15.9 - - - +
12B MET* 4.0 9.6 - - + -
63B ILE* 3.7 0.2 - - - -
64B TYR* 2.9 58.8 + - + +
66B HIS* 3.5 24.9 - - + +
67B GLY* 1.3 77.3 - - - +
69B VAL* 1.3 63.2 + - - +
70B LEU* 3.7 24.2 - - + -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 3.8 1.2 - - - +
10B ASP* 3.5 1.4 - - - -
11B PHE* 2.7 62.8 + - + +
13B LEU* 4.1 18.8 - - + -
22B ILE* 3.9 26.2 - - + -
26B LEU* 4.3 11.7 - - + -
61B LEU* 3.9 25.4 - - + -
62B ARG 3.5 3.8 - - - +
63B ILE* 4.1 12.6 - - + -
67B GLY* 5.0 0.4 - - - -
68B LEU* 1.3 79.4 - - - +
70B LEU* 1.3 65.3 + - - +
71B LEU* 5.3 0.9 - - + +
97B MET* 4.6 2.0 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 4.1 7.9 - - - +
74A GLN* 3.7 23.1 - - - +
116A ARG* 3.4 37.2 - - + +
9B LEU 3.5 2.5 - - - -
10B ASP* 3.3 31.9 - - + +
60B ASN 3.8 1.0 - - - +
61B LEU* 3.6 3.0 - - - -
62B ARG* 2.8 43.2 + - + +
64B TYR* 3.8 17.5 - - + -
68B LEU* 3.7 26.2 - - + -
69B VAL* 1.3 82.6 - - - +
71B LEU* 1.3 59.0 + - - +
72B ASP* 4.5 2.1 - - - +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 3.3 5.0 + - - -
8B THR* 3.3 3.3 - - - -
9B LEU* 2.9 43.5 + - + +
11B PHE* 5.7 2.0 - - + -
26B LEU* 6.3 0.2 - - + -
30B PHE* 3.7 25.4 - - + -
59B ALA* 4.4 2.0 - - + -
60B ASN 3.2 18.8 - - - +
61B LEU* 3.9 22.9 - - + -
69B VAL* 5.8 1.3 - - + -
70B LEU* 1.3 74.6 - - - +
72B ASP* 1.3 64.2 + - - +
73B LEU* 3.7 12.3 - - + +
89B ILE* 5.6 0.2 - - + -
90B LEU* 3.5 30.3 - - + -
93B VAL* 3.9 33.2 - - + -
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A HIS* 3.6 6.7 + - - -
58A PHE* 6.3 0.7 - - - -
72A ASP* 5.5 0.3 - - - -
74A GLN* 4.2 8.4 + - - -
116A ARG* 2.7 38.3 + - - -
6B HIS* 2.7 36.2 + - + -
7B SER 3.4 3.8 - - - -
8B THR* 4.0 1.4 - - - +
58B PHE* 4.6 2.7 - - + -
59B ALA* 3.1 6.6 - - - +
60B ASN* 2.7 48.2 + - + +
70B LEU 4.5 1.9 - - - +
71B LEU* 1.3 75.7 + - - +
73B LEU* 1.3 66.7 + - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG 3.4 1.0 - - - +
6B HIS* 3.2 8.4 + - - -
7B SER* 2.8 37.2 + - - -
30B PHE* 5.1 0.4 - - + -
35B MET* 5.4 4.0 - - + -
57B SER* 5.9 1.8 - - - +
58B PHE 3.4 6.3 - - - +
59B ALA* 3.7 18.4 - - + -
71B LEU* 3.7 15.9 - - + -
72B ASP* 1.3 83.0 - - - +
74B GLN* 1.3 59.9 + - - +
86B ILE* 3.7 42.8 - - + -
89B ILE* 4.3 26.0 - - + -
90B LEU* 3.4 29.6 - - + -
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 4.6 2.6 - - - +
64A TYR* 3.4 20.9 - - + +
70A LEU* 3.3 30.3 - - - +
72A ASP* 4.1 5.3 + - - -
4B SER* 4.0 7.3 + - - +
5B ARG 3.3 4.3 - - - -
6B HIS* 3.7 16.7 + - + +
56B GLY 5.6 0.2 - - - -
57B SER* 3.4 8.7 - - - -
58B PHE* 2.9 64.7 + - + +
73B LEU* 1.3 76.6 - - - +
75B SER* 1.3 62.4 + - - +
86B ILE* 4.4 3.3 - - - +
116B ARG* 3.6 33.1 - - - +
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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