Contacts of the strand formed by residues 56 - 61 (chain G) in PDB entry 6C6S
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 VAL 56 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G ALA* 1.3 77.1 - - + +
57G THR* 1.3 62.5 + - - +
58G GLU 4.5 0.9 - - - +
59G VAL* 4.3 19.3 - - + -
85G LEU* 3.2 36.3 - - + +
86G LYS* 3.9 8.3 - - - +
88G LEU* 4.8 7.6 + - + +
90G VAL* 5.2 1.9 - - + +
144G ILE* 3.6 29.8 - - + -
145G LYS 4.1 4.9 - - - +
146G VAL* 4.1 8.7 - - + +
173G VAL* 3.6 20.7 - - + +
174G ASP 4.1 8.2 - - - +
175G ALA* 4.1 9.2 - - - +
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Residues in contact with THR 57 (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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55G ALA 3.9 1.6 + - - -
56G VAL* 1.3 77.3 + - - +
58G GLU* 1.3 73.6 + - + +
145G LYS* 2.8 21.5 + - + +
147G GLN* 3.2 42.7 + - - +
158G ARG* 3.4 31.8 + - - +
172G LEU* 3.9 0.2 - - - -
173G VAL* 3.1 33.4 + - - +
175G ALA* 4.9 1.5 - - + +
177G TYR* 3.6 8.4 + - - +
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Residues in contact with GLU 58 (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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56G VAL* 4.5 0.4 - - - +
57G THR* 1.3 93.6 - - + +
59G VAL* 1.3 63.6 + - - +
143G ARG 3.7 1.0 - - - +
144G ILE* 3.6 0.9 - - - -
145G LYS* 2.6 58.1 + - + +
158G ARG* 3.9 14.3 + - - +
170G ARG* 2.5 46.6 + - + +
171G LEU 3.4 13.7 - - - +
172G LEU* 4.1 19.7 - - + +
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Residues in contact with VAL 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G VAL* 4.3 12.3 - - + -
58G GLU* 1.3 79.0 - - - +
60G GLU* 1.3 63.5 + - - +
61G ILE* 3.7 23.8 - - + -
82G LEU* 3.8 20.6 - - + -
85G LEU* 3.7 22.2 - - + -
142G MET* 3.7 26.0 - - + -
143G ARG 3.6 4.3 - - - +
144G ILE* 4.7 3.8 - - + +
170G ARG* 3.8 0.7 - - - -
171G LEU* 2.9 36.4 + - + +
172G LEU* 5.0 0.2 - - - +
173G VAL* 3.8 14.4 - - + -
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Residues in contact with GLU 60 (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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59G VAL* 1.3 75.4 - - - +
61G ILE* 1.3 70.4 + - - +
62G ASP* 3.8 0.7 + - - -
141G SER 4.1 0.7 - - - +
142G MET* 3.3 2.0 - - - -
143G ARG* 2.9 76.6 + - + +
167G PRO* 5.7 0.7 - - - +
169G GLY* 4.1 19.0 - - - +
170G ARG* 3.3 35.4 + - + +
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Residues in contact with ILE 61 (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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59G VAL* 3.7 18.8 - - + -
60G GLU* 1.3 80.9 - - - +
62G ASP* 1.3 68.5 + - - +
63G GLY 3.7 2.9 - - - +
64G VAL* 3.8 38.7 - - + +
71G LYS* 4.7 14.6 - - + -
78G ILE* 4.2 18.8 - - + -
81G ILE* 5.2 5.8 - - + -
82G LEU* 4.6 3.8 - - + -
140G ILE* 5.2 3.4 - - + -
141G SER 4.5 8.7 - - - +
142G MET* 3.9 32.3 - - + -
169G GLY* 4.9 4.5 + - - +
171G LEU* 3.8 26.8 - - + +
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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