Contacts of the strand formed by residues 660 - 664 (chain A) in PDB entry 3DPK
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 LEU 660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579A ARG* 3.7 23.3 - - + +
582A LEU* 4.0 9.9 - - + -
584A PHE* 3.8 23.8 - - + -
615A VAL* 3.9 8.7 - - + -
616A LYS 3.4 2.0 - - - -
617A MET* 3.6 34.3 - - + -
652A ALA* 3.2 6.6 - - - +
653A CYS* 2.8 54.9 + - + +
658A PRO* 3.6 17.0 - - + +
659A VAL* 1.3 82.3 - - - +
661A VAL* 1.3 64.5 + - - +
662A ILE* 4.1 0.9 - - + -
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Residues in contact with VAL 661 (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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614A ALA 3.6 0.9 - - - +
615A VAL* 3.3 3.5 - - - -
616A LYS* 2.8 48.2 + - + +
630A LEU* 3.9 32.1 - - + +
633A GLU* 5.5 3.4 - - + +
634A LEU* 3.9 26.5 - - + +
637A MET* 4.6 8.1 - - - -
649A LEU* 3.6 26.0 - - + -
651A GLY 4.0 2.5 - - - +
652A ALA* 4.5 0.2 - - - +
659A VAL* 4.4 5.2 - - + -
660A LEU* 1.3 77.3 - - - +
662A ILE* 1.3 62.1 + - - +
663A THR* 4.0 12.9 + - + +
923A 8C5 5.3 2.5 - - - +
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Residues in contact with ILE 662 (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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577A PHE* 3.7 36.1 - - + -
582A LEU* 4.0 20.9 - - + -
604A LEU* 4.4 7.0 - - + -
613A VAL* 3.9 35.7 - - + -
614A ALA 3.4 3.6 - - - +
615A VAL* 4.6 7.2 - - + +
649A LEU* 3.7 1.6 - - - +
650A LEU* 2.8 32.0 + - + -
651A GLY* 2.9 34.7 + - - +
652A ALA* 4.0 3.4 - - - +
653A CYS* 4.1 6.5 - - - -
660A LEU 4.7 2.2 - - - +
661A VAL* 1.3 76.8 - - - +
663A THR* 1.3 65.4 + - - +
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Residues in contact with THR 663 (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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613A VAL* 3.6 8.0 - - - +
614A ALA* 2.8 37.1 + - - +
616A LYS* 5.9 0.7 + - + +
637A MET* 3.7 19.3 - - + -
647A VAL* 3.8 5.2 - - - -
648A ASN 3.3 10.1 - - - +
649A LEU* 4.3 1.6 - - - -
650A LEU* 3.7 6.5 - - - +
661A VAL* 4.3 10.0 + - + +
662A ILE* 1.3 80.0 - - - +
664A GLU* 1.3 60.0 + - - +
665A TYR 3.5 0.3 + - - -
923A 8C5 2.5 60.0 + - - +
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Residues in contact with GLU 664 (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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642A GLN* 5.8 0.5 + - - -
647A VAL* 3.6 10.8 - - + +
648A ASN* 3.0 49.4 + - + +
650A LEU* 3.8 22.9 - - + +
663A THR* 1.3 77.6 - - - +
665A TYR* 1.3 62.8 + - - +
666A CYS* 3.9 1.1 + - - -
793A LYS* 2.9 38.6 + - + +
923A 8C5 3.2 19.9 - - - -
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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