Contacts of the strand formed by residues 708 - 712 (chain A) in PDB entry 5L6P
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 MET 708 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633A VAL* 4.8 12.8 - - + -
635A ILE* 4.8 10.8 - - - -
664A ILE* 3.8 14.1 - - + -
665A LYS 3.2 11.2 - - - +
666A THR* 3.8 17.7 - - + -
679A PHE* 4.6 1.1 - - - -
700A VAL* 3.4 9.8 - - - +
701A VAL* 2.8 67.9 + - + +
704A SER* 4.1 6.5 - - - +
706A PRO* 3.5 20.9 - - + +
707A VAL* 1.4 78.8 - - - +
709A ILE* 1.3 63.4 + - - +
710A LEU* 3.9 13.0 - - + -
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Residues in contact with ILE 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663A ALA 3.6 1.7 - - - +
664A ILE* 3.5 4.0 - - - -
665A LYS* 2.9 56.5 + - + +
679A PHE* 3.4 54.7 - - + +
680A LEU* 4.9 0.7 - - + +
682A GLU 5.3 0.4 - - - -
683A ALA* 3.8 25.4 - - + +
686A MET* 5.1 3.6 - - - -
697A LEU* 3.7 20.6 - - + -
699A GLY 4.1 3.1 - - - -
700A VAL* 4.4 7.2 - - + +
708A MET* 1.3 74.8 - - - +
710A LEU* 1.3 60.4 + - - +
711A THR* 4.1 10.5 + - + -
1001A 6P8 4.8 6.0 - - + -
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Residues in contact with LEU 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A VAL* 3.8 26.9 - - + -
652A LEU* 4.6 11.9 - - + -
662A VAL* 5.2 6.5 - - + -
663A ALA 3.6 4.3 - - - +
664A ILE* 3.8 37.2 - - + -
697A LEU* 3.7 2.1 - - - +
698A GLU* 2.8 34.7 + - + -
699A GLY* 2.8 34.4 + - - +
700A VAL 5.5 0.2 - - - -
701A VAL* 4.1 20.0 - - + -
708A MET* 3.9 14.1 - - + -
709A ILE* 1.3 74.3 - - - +
711A THR* 1.3 57.7 + - - +
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Residues in contact with THR 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A VAL* 3.4 5.8 - - - +
663A ALA* 2.7 38.9 + - - +
686A MET* 3.6 27.6 - - + -
695A ILE* 4.3 8.2 - - - +
696A ARG 3.4 17.3 - - - +
697A LEU* 3.9 13.0 - - + -
698A GLU* 4.1 7.2 - - - +
709A ILE* 4.1 4.5 + - + -
710A LEU* 1.3 78.9 - - - +
712A GLU* 1.4 57.3 + - - +
1001A 6P8 3.5 34.3 + - + -
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Residues in contact with GLU 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A PHE 4.5 4.0 - - - +
662A VAL* 4.5 2.2 - - - -
695A ILE* 3.7 9.1 - - + +
696A ARG* 3.4 52.1 + - + +
698A GLU* 3.9 17.6 - - - +
711A THR* 1.4 73.3 - - - +
713A PHE* 1.4 62.2 + - - +
714A MET* 3.7 10.1 - - - +
773A LYS* 2.8 45.9 + - - +
1001A 6P8 3.3 18.2 - - - -
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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