Contacts of the strand formed by residues 31 - 39 (chain G) in PDB entry 4FAO
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 GLU 31 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14G ARG* 3.9 34.5 + - + +
15G VAL 3.2 15.3 - - - +
16G ASN* 3.6 25.2 + - + +
17G PHE* 4.6 2.7 - - - +
29G PRO* 3.3 10.6 - - - +
30G LYS* 1.3 81.8 - - + +
32G TYR* 1.3 63.0 + - - +
64K PHE* 4.0 11.8 - - + -
65K ASN* 3.0 28.6 + - - +
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Residues in contact with TYR 32 (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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14G ARG* 3.6 1.4 - - - -
15G VAL* 2.9 51.7 + - + -
17G PHE* 3.5 35.0 - + - -
29G PRO* 3.9 14.8 - - + -
31G GLU* 1.3 77.2 - - - +
33G GLU* 1.3 67.1 + - - +
34G ALA* 3.2 25.1 + - + +
82G ILE* 3.7 28.7 - - + -
102G MET* 2.8 51.2 + - + +
57H VAL* 3.9 13.3 - - + +
63K ASP* 4.6 6.1 - - + +
64K PHE* 3.5 12.3 - - - -
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Residues in contact with GLU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G SER* 2.9 21.5 + - - -
13G LEU 2.5 35.4 + - - -
14G ARG* 3.1 17.4 + - - +
32G TYR* 1.3 79.6 - - - +
34G ALA* 1.3 66.6 + - - +
35G TYR* 3.3 39.8 + - + +
82G ILE* 5.2 0.7 - - - +
103G SER* 3.1 18.0 + - - -
64K PHE* 3.2 26.2 - - + -
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Residues in contact with ALA 34 (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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13G LEU* 2.6 22.3 + - + +
15G VAL* 4.0 11.2 - - + -
32G TYR* 3.2 35.0 + - + +
33G GLU* 1.3 93.6 - - - +
35G TYR* 1.3 64.1 + - - +
102G MET 3.3 11.9 - - - +
103G SER* 4.1 1.6 - - - -
54H HIS* 4.1 10.8 - - + +
57H VAL* 5.4 1.6 - - + -
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Residues in contact with TYR 35 (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 LYS* 3.3 35.3 + - + -
11G THR 3.1 22.4 - - - +
12G SER* 4.4 3.4 - - - -
13G LEU* 3.7 10.7 - - - +
33G GLU* 3.3 36.8 + - + +
34G ALA* 1.3 77.4 - - - +
36G GLU* 1.3 61.1 + - - +
103G SER* 3.6 13.0 - - - -
104G VAL* 3.1 49.7 - - + +
54H HIS* 3.0 22.3 + - - -
67K TYR* 5.5 2.4 + - - -
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Residues in contact with GLU 36 (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 LYS* 3.6 4.7 - - - -
11G THR* 2.9 44.1 + - - +
12G SER 4.7 0.3 - - - +
13G LEU* 3.9 20.6 - - + +
35G TYR* 1.3 76.2 - - - +
37G CYS* 1.3 68.8 + - - +
38G LYS* 3.0 47.9 + - + +
104G VAL* 4.9 0.9 - - - -
58H GLN* 4.3 20.6 + - - +
68H LYS 3.9 5.7 - - - +
69H VAL* 3.7 10.4 - - - -
70H GLY* 3.5 24.1 + - - -
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Residues in contact with CYS 37 (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 GLN 3.7 3.1 - - - -
36G GLU* 1.3 77.8 - - - +
38G LYS* 1.3 61.2 + - - +
39G GLY 4.4 0.2 + - - -
74G CYS* 3.5 31.5 - - - +
75G VAL* 3.6 5.6 - - - -
76G PRO* 3.5 34.6 - - + +
104G VAL* 3.9 10.5 - - - +
107G CYS* 2.0 45.1 - - - -
58H GLN* 4.9 6.5 + - - +
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Residues in contact with LYS 38 (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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94E ARG* 3.5 43.6 - - - +
7G HIS 3.7 0.5 - - - +
8G CYS* 3.5 0.7 - - - -
9G GLN* 2.9 35.5 + - + +
11G THR* 3.7 34.0 - - + +
12G SER 5.1 0.8 + - - -
36G GLU* 3.0 42.9 + - + +
37G CYS* 1.3 74.7 - - - +
39G GLY* 1.3 61.3 + - - +
74G CYS* 3.8 1.9 - - - -
68H LYS 3.9 12.1 + - - -
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Residues in contact with GLY 39 (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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71E GLU* 3.4 20.8 + - - +
94E ARG* 6.2 0.2 - - - +
6G SER 5.0 0.2 - - - -
7G HIS 2.5 19.1 - - - -
8G CYS* 4.0 2.5 - - - -
38G LYS* 1.3 74.6 - - - +
40G GLY* 1.3 61.3 + - - -
41G CYS* 4.9 0.2 - - - -
74G CYS* 3.4 20.3 + - - +
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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