Contacts of the strand formed by residues 898 - 902 (chain G) in PDB entry 6C3P
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 TRP 898 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702G ARG* 3.2 35.4 + - + +
703G ILE* 4.9 0.4 - - + -
704G PRO* 4.4 25.8 - - + -
707G GLN* 5.2 2.9 - - + +
708G LEU 3.2 3.8 + - - +
709G THR* 2.8 48.6 + - + +
710G MET 3.0 3.8 + - - -
896G ALA* 3.8 2.3 - - - +
897G ASP* 1.3 81.6 - - + +
899G ILE* 1.3 82.7 + - - +
900G ILE* 3.5 17.4 - - + +
910G GLU* 3.4 21.2 - - + +
911G GLY* 3.8 24.9 - - - -
912G THR 4.9 1.6 - - - +
915G ASP* 4.9 3.6 - - - -
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Residues in contact with ILE 899 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710G MET* 3.4 10.8 - - + +
712G VAL* 4.8 8.3 - - + -
893G LEU* 3.5 47.6 - - + +
896G ALA* 4.0 9.6 - - + +
898G TRP* 1.3 89.8 + - - +
900G ILE* 1.3 75.5 + - - +
901G ALA* 4.7 3.6 - - + +
909G ARG 6.3 0.2 - - - -
910G GLU* 3.1 30.5 - - - +
911G GLY 3.6 11.9 + - - +
912G THR* 4.1 30.3 - - - +
916G PHE* 6.1 0.9 - - + -
926G HIS* 6.2 2.0 - - + -
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Residues in contact with ILE 900 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701G ILE* 4.8 15.3 - - + -
702G ARG 4.9 2.2 - - - +
703G ILE* 4.8 9.0 - - + -
709G THR* 3.1 31.4 - - + +
710G MET 2.7 13.2 + - - +
711G ILE* 3.2 23.8 - - + +
712G VAL* 3.1 28.4 + - - +
722G LEU* 5.2 0.9 - - + -
898G TRP* 3.5 17.9 - - + +
899G ILE* 1.3 78.2 - - - +
901G ALA* 1.3 62.5 + - - +
902G MET* 3.7 26.5 - - + -
907G ILE* 4.1 16.8 - - + -
909G ARG 3.7 5.4 - - - +
910G GLU* 4.9 2.9 - - + -
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Residues in contact with ALA 901 (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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712G VAL* 3.8 14.4 - - + +
713G GLY* 6.3 0.2 - - - -
899G ILE* 4.3 4.7 - - + -
900G ILE* 1.3 74.3 - - - +
902G MET* 1.3 54.3 + - - +
907G ILE* 3.3 5.0 - - - +
908G GLN* 2.4 37.4 + - + -
909G ARG* 3.0 32.4 + - + +
922G GLN* 4.8 7.2 - - - +
926G HIS* 5.9 5.6 - - + +
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Residues in contact with MET 902 (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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696G LEU* 5.6 2.9 - - - -
699G ILE* 6.3 1.1 - - + -
711G ILE* 3.6 22.4 - - + -
712G VAL 3.3 8.6 + - - +
713G GLY* 3.2 26.3 - - - -
717G CYS* 3.8 15.6 - - - +
718G GLY* 3.2 29.2 - - - +
719G LYS* 3.6 9.2 - - - -
722G LEU* 3.6 31.6 - - + -
900G ILE* 3.7 15.0 - - + -
901G ALA* 1.3 74.4 - - - +
903G LYS* 1.3 64.3 + - - +
906G THR 3.2 21.5 - - - +
907G ILE* 3.6 10.3 - - + -
908G GLN* 3.8 4.5 - - - -
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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