Contacts of the strand formed by residues 560 - 567 (chain A) in PDB entry 3AR2
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 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A LYS* 3.7 12.2 - - - +
353A THR* 3.9 10.0 + - - +
361A MET* 3.1 23.7 - - + +
441A THR* 2.8 34.6 + - + +
558A THR 3.8 2.0 + - - -
559A LEU* 1.3 68.8 - - - +
561A CYS* 1.3 65.6 + - - +
562A LEU* 5.3 1.7 - - + +
597A VAL 3.7 0.9 - - - +
598A GLY* 3.6 0.9 - - - -
599A MET* 2.7 50.8 + - + +
601A ASP* 5.3 6.3 - - + -
627A ASP* 2.9 36.6 + - - +
631A THR* 4.8 3.1 - - - -
1002A ACP 2.5 70.0 + - - -
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Residues in contact with CYS 561 (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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518A PRO* 3.3 29.1 - - + +
549A ILE* 4.1 30.7 - - + -
552A TRP* 4.3 15.0 - - - -
553A GLY* 4.8 1.1 - - - -
559A LEU 3.7 10.8 + - - +
560A ARG* 1.3 80.1 - - - +
562A LEU* 1.3 68.7 + - - +
596A VAL* 4.3 9.9 - - + -
597A VAL 3.4 3.8 - - - -
598A GLY* 4.0 17.0 - - - -
627A ASP* 4.8 4.8 + - - +
628A ASN* 6.3 3.0 - - + +
631A THR* 5.1 3.4 - - + +
678A ARG* 4.7 3.5 + - - -
1002A ACP 4.0 4.9 + - - -
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Residues in contact with LEU 562 (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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441A THR* 4.3 21.3 - - + -
445A LEU* 3.9 33.7 - - + -
515A LYS* 3.9 21.3 - - + -
516A GLY 3.6 17.7 - - - +
518A PRO* 3.9 3.8 - - - -
560A ARG* 5.6 2.9 - - + +
561A CYS* 1.3 76.2 - - - +
563A ALA* 1.3 61.3 + - - +
564A LEU* 3.7 5.2 - - + +
596A VAL* 3.3 6.0 - - - +
597A VAL* 3.0 41.6 + - + -
599A MET* 4.5 4.3 - - + -
1002A ACP 3.6 39.9 - - + +
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Residues in contact with ALA 563 (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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515A LYS* 3.2 7.3 - - - +
516A GLY 2.9 29.9 + - - +
518A PRO* 3.7 13.1 - - + +
521A VAL* 3.7 18.0 - - + +
522A ILE* 3.4 33.4 - - + -
562A LEU* 1.3 74.2 - - - +
564A LEU* 1.3 63.6 + - - +
593A PHE* 4.6 1.3 - - + -
595A GLY 3.6 5.8 - - - +
596A VAL* 4.3 4.0 - - + -
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Residues in contact with LEU 564 (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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413A LEU* 3.9 15.7 - - + +
416A ILE* 3.8 31.0 - - + -
417A CYS* 3.5 30.7 - - - +
445A LEU* 5.5 1.6 - - + -
514A VAL 3.6 3.1 - - - -
515A LYS* 4.5 11.0 - - + -
521A VAL* 4.9 0.7 - - - -
562A LEU* 3.7 17.7 - - + +
563A ALA* 1.3 78.0 - - - +
565A ALA* 1.3 62.1 + - - +
593A PHE* 4.1 2.3 - - - -
594A VAL* 2.8 25.6 + - - +
595A GLY 2.8 29.9 + - - +
597A VAL* 3.8 26.0 - - + -
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Residues in contact with ALA 565 (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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416A ILE* 3.5 3.0 - - - +
514A VAL* 2.7 41.4 + - + +
521A VAL* 3.9 12.7 - - + +
525A CYS* 3.9 19.5 - - - -
563A ALA 4.3 0.2 - - - -
564A LEU* 1.3 75.6 - - - +
566A THR* 1.3 63.6 + - - +
591A LEU* 4.0 9.4 - - + -
592A THR 3.0 23.3 - - - +
593A PHE* 4.2 0.4 - - - -
594A VAL* 4.1 1.8 - - - -
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Residues in contact with THR 566 (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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412A GLU* 3.0 29.9 + - - +
416A ILE* 3.2 28.7 - - + -
511A LYS* 5.0 3.5 - - - +
512A MET 3.1 11.9 - - - -
513A PHE* 3.3 23.5 - - + -
514A VAL 4.4 0.9 - - - +
529A ARG* 3.5 9.9 + - - -
565A ALA* 1.3 72.2 - - - +
567A ARG* 1.3 59.0 + - - +
568A ASP* 3.5 8.5 + - - -
591A LEU* 4.3 4.3 - - - -
592A THR* 2.8 35.6 + - - -
594A VAL* 3.9 0.9 - - + -
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Residues in contact with ARG 567 (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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511A LYS* 3.7 3.1 - - - +
512A MET* 2.8 42.6 + - + -
566A THR* 1.3 70.3 - - - +
568A ASP* 1.3 66.0 + - - +
569A THR* 2.7 29.4 + - - +
570A PRO* 3.3 25.3 - - - +
571A PRO* 3.5 21.9 - - - +
586A GLU 4.2 9.9 + - - -
587A TYR 3.2 23.5 + - - +
589A THR* 3.3 33.3 + - - +
590A ASP* 3.8 23.6 + - - +
591A LEU* 4.0 11.0 - - + +
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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