Contacts of the strand formed by residues 668 - 672 (chain A) in PDB entry 4I1R
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 668 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A ILE 3.7 0.9 - - - +
615A TYR* 3.3 6.1 - - - -
616A THR* 3.0 38.2 + - - +
629A ASP* 3.8 33.9 - - + +
630A ALA 3.5 21.5 - - - +
631A TYR* 4.3 14.4 - - + +
632A VAL* 6.0 0.5 - - - +
647A ASN* 3.4 36.5 - - + +
648A LYS 3.3 17.7 - - - +
649A GLY* 4.4 3.4 - - - +
667A CYS* 1.3 79.8 - - - +
669A TYR* 1.3 60.9 + - - +
670A THR* 5.3 0.2 + - - -
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Residues in contact with TYR 669 (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 ILE* 3.7 19.5 - - + -
614A ILE 3.4 1.1 - - - -
615A TYR* 3.5 22.7 - - + -
646A ALA* 3.8 1.9 - - - -
647A ASN 2.9 18.9 + - - -
648A LYS* 3.0 21.3 + - - +
649A GLY 4.2 5.8 - - - -
650A THR* 3.7 9.4 - - - +
651A PRO* 3.5 45.8 - - + +
654A THR* 4.3 8.3 + - - +
660A SER 5.0 0.9 + - - -
663A LEU* 3.4 34.3 + - + +
664A PRO 2.3 34.0 + - - -
665A LYS* 4.6 1.9 - - - -
666A HIS 5.8 0.2 - - - -
667A CYS* 3.8 22.1 - - + +
668A LEU* 1.3 74.5 - - - +
670A THR* 1.3 61.0 + - - +
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Residues in contact with THR 670 (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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612A MET 4.0 0.5 - - - +
613A ILE* 3.6 2.7 - - - -
614A ILE* 2.7 43.7 + - - +
632A VAL* 3.3 23.5 - - - +
635A PHE* 3.9 24.9 - - + -
641A ILE* 4.6 5.4 - - + -
646A ALA* 3.5 22.4 - - + +
647A ASN* 3.0 24.3 + - - +
654A THR* 4.8 1.8 - - - -
668A LEU 5.3 0.2 + - - -
669A TYR* 1.3 70.5 - - - +
671A ARG* 1.3 62.1 + - - +
672A LEU* 4.0 13.8 + - + -
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Residues in contact with ARG 671 (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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363A LEU* 3.5 21.8 - - - +
384A LEU* 3.7 17.0 - - - +
385A ASP* 5.7 1.2 + - - -
607A GLU* 2.7 36.7 + - - +
608A PHE* 4.5 0.2 - - - -
611A VAL* 3.4 23.6 - - + +
612A MET 3.5 5.6 - - - +
613A ILE* 4.2 8.5 - - + +
641A ILE* 3.9 16.0 - - - +
645A ASP 5.5 0.2 + - - -
654A THR* 3.0 35.5 + - + +
655A GLY 3.7 16.2 + - - +
656A SER* 3.5 17.4 - - - +
670A THR* 1.3 72.9 - - - +
672A LEU* 1.3 66.9 + - - +
673A SER* 3.3 23.0 + - - +
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Residues in contact with LEU 672 (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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610A ASN 3.2 13.2 - - - +
611A VAL* 4.4 0.4 - - - -
612A MET* 2.7 34.8 + - + +
614A ILE* 3.6 22.0 - - + -
635A PHE* 3.9 27.6 - - + -
639A LEU* 4.7 10.8 - - + -
641A ILE* 4.4 15.7 - - + -
670A THR* 4.0 15.5 - - + -
671A ARG* 1.3 77.6 - - - +
673A SER* 1.3 62.0 + - - +
674A SER 3.5 2.9 - - - +
675A LEU* 3.4 18.6 - - + +
682A LEU* 3.6 32.5 - - + -
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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