Contacts of the strand formed by residues 664 - 670 (chain I) in PDB entry 5A31
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 ARG 664 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639I LEU* 3.6 21.0 - - + +
652I VAL* 5.4 2.0 - - + -
653I LEU 3.3 11.0 - - - +
654I LYS* 4.0 24.6 - - + +
661I GLY 5.0 0.4 + - - -
662I ARG 3.7 1.8 - - - -
663I ASP* 1.3 111.3 + - - +
665I LEU* 1.3 62.7 + - - +
713I LEU* 3.9 3.1 - - - +
714I LEU* 2.9 43.7 + - + +
718I LYS* 3.5 42.0 + - - +
719I ALA 2.9 27.6 + - - +
720I GLN* 3.9 9.5 + - - -
736I SER* 4.7 6.7 - - - -
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Residues in contact with LEU 665 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623I PHE* 3.9 45.5 - - + -
632I ARG* 5.6 6.5 - - - +
636I TYR* 4.0 28.3 - - + +
651I VAL 3.8 0.3 - - - +
652I VAL* 3.4 8.1 - - - +
653I LEU* 2.9 38.0 + - + +
655I ASP* 4.3 8.3 - - + +
662I ARG 5.6 0.7 - - - +
663I ASP 4.1 7.9 - - - +
664I ARG* 1.3 84.1 - - - +
666I LEU* 1.3 59.6 + - - +
667I VAL* 4.1 7.9 + - + +
711I TRP* 4.5 12.3 - - + -
712I ARG 3.5 10.1 - - - +
713I LEU* 4.8 11.4 - - + -
714I LEU* 4.1 4.7 - - - -
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Residues in contact with LEU 666 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I PHE* 4.4 6.2 - - + -
650I THR* 3.6 31.4 - - + -
651I VAL 3.6 7.2 - - - +
652I VAL* 3.9 2.5 - - + -
665I LEU* 1.3 71.9 - - - +
667I VAL* 1.3 60.7 + - - +
711I TRP* 3.1 5.9 - - - +
712I ARG* 2.9 38.6 + - + +
714I LEU* 3.9 19.5 - - + +
722I VAL* 3.9 15.9 - - + -
731I SER* 6.1 1.6 - - - -
733I VAL* 4.1 11.2 - - + -
744I PHE* 4.0 34.3 - - + -
746I MET* 3.9 24.5 - - + -
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Residues in contact with VAL 667 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620I PHE* 4.6 7.2 - - + -
623I PHE* 3.5 32.5 - - + -
650I THR* 3.7 1.2 - - - -
651I VAL* 2.9 46.0 + - + +
653I LEU* 3.7 22.2 - - + -
665I LEU* 4.2 11.0 - - + +
666I LEU* 1.3 81.1 - - - +
668I GLN* 1.3 67.9 + - - +
669I LEU 3.7 0.6 + - - +
707I PHE* 3.8 33.2 - - + -
711I TRP* 4.1 7.0 - - + -
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Residues in contact with GLN 668 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I PHE* 3.5 28.1 - - + -
644I TYR* 3.4 43.0 - - - +
648I THR* 4.7 10.6 + - + +
649I VAL 4.9 0.4 - - - -
650I THR* 2.8 36.2 + - - +
666I LEU 4.4 0.2 + - - -
667I VAL* 1.3 73.1 - - - +
669I LEU* 1.3 59.1 + - - +
670I PRO* 3.6 6.4 - - + +
707I PHE* 3.5 18.5 - - - -
709I LYS 4.9 0.7 - - - +
710I HIS* 3.1 28.5 + - + +
746I MET* 4.1 11.6 + - + +
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Residues in contact with LEU 669 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598I MET* 4.0 27.1 - - + -
600I ILE* 4.7 6.1 - - + -
618I ILE* 4.4 19.7 - - + -
620I PHE* 4.7 2.7 - - + -
648I THR* 3.4 5.1 - - - -
649I VAL* 2.9 52.9 + - + +
651I VAL* 3.9 14.1 - - + -
668I GLN* 1.3 72.7 - - - +
670I PRO* 1.4 71.6 - - + +
671I LEU* 3.7 2.1 + - + -
674I VAL* 3.5 18.2 - - + -
705I MET* 3.3 30.3 - - + -
707I PHE* 4.2 9.9 - - + -
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Residues in contact with PRO 670 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647I GLU 3.8 5.4 - - - +
648I THR* 3.9 12.3 - - + -
668I GLN* 3.6 9.6 - - + +
669I LEU* 1.4 88.5 - - + +
671I LEU* 1.3 65.4 + - - +
672I SER* 3.2 14.4 - - - +
673I LEU* 3.4 32.8 + - + +
674I VAL* 3.6 13.7 + - - +
705I MET* 5.9 0.9 - - - -
707I PHE* 4.2 9.4 - - + -
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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
------------------------------------------------------------
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