Contacts of the strand formed by residues 591 - 604 (chain A) in PDB entry 6CIM
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 PHE 591 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574A ILE* 4.3 15.7 - - + -
578A MET* 3.6 29.6 - - - -
587A LEU 4.3 7.2 - - - -
588A ASN 4.5 1.1 - - - -
589A GLY 3.1 10.7 + - - -
590A PRO* 1.3 74.9 - - - +
592A THR* 1.3 55.5 + - - +
629A ILE* 4.0 15.7 - - + -
630A THR 3.2 16.2 - - - +
631A ILE* 3.6 27.4 - - + -
640A VAL* 4.4 5.8 - - + -
691A MET* 5.7 1.6 - - + -
696A ARG* 4.0 27.1 - - + -
697A THR 2.9 16.0 + - - -
698A PHE* 3.2 36.6 - + + -
699A LYS* 2.7 33.1 + - - +
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Residues in contact with THR 592 (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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590A PRO* 4.6 3.8 + - - +
591A PHE* 1.3 74.4 + - - +
593A VAL* 1.3 65.4 + - - +
594A VAL* 4.8 4.6 - - + +
628A ARG 3.7 1.6 - - - +
629A ILE* 3.1 7.5 - - - +
630A THR* 2.9 46.7 + - - +
699A LYS* 3.2 19.6 - - + +
701A ILE* 3.8 33.0 - - + -
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Residues in contact with VAL 593 (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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567A LEU* 4.5 9.9 - - + -
592A THR* 1.3 77.8 - - - +
594A VAL* 1.3 63.5 + - - +
595A VAL* 3.5 21.4 + - + -
626A VAL* 4.0 27.1 - - + -
628A ARG 3.6 3.1 - - - +
629A ILE* 4.3 9.6 - - + +
698A PHE* 4.0 26.5 - - + -
699A LYS 2.8 11.3 + - - +
700A PHE* 3.4 30.8 - - + -
701A ILE* 2.9 27.5 + - - +
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Residues in contact with VAL 594 (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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592A THR* 4.8 6.5 - - + +
593A VAL* 1.3 73.2 - - - +
595A VAL* 1.3 61.4 + - - +
626A VAL* 3.8 0.9 - - - -
627A MET* 2.8 39.9 + - + +
628A ARG* 2.9 51.6 + - + +
630A THR* 5.9 2.2 - - + +
701A ILE* 3.6 23.8 - - + +
703A ARG* 3.9 28.0 - - - -
956A TRP* 5.1 3.8 - - + -
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Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A TYR* 4.0 3.8 - - - +
563A LEU* 3.9 21.3 - - + -
593A VAL* 3.8 24.7 - - + +
594A VAL* 1.3 72.4 - - - +
596A LYS* 1.3 63.7 + - - +
597A GLU* 4.6 0.9 - - + +
624A PHE* 3.7 33.2 - - + -
625A THR 3.8 3.4 - - - +
626A VAL* 4.7 6.1 - - + -
627A MET* 4.7 0.2 - - - -
700A PHE* 4.1 9.6 - - + -
701A ILE 2.9 10.2 + - - +
702A PHE* 3.9 26.5 - - + -
703A ARG* 2.9 28.4 + - - +
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Residues in contact with LYS 596 (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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594A VAL 3.8 2.0 + - - -
595A VAL* 1.3 72.4 - - - +
597A GLU* 1.3 65.2 + - - +
598A SER* 4.0 11.6 + - - +
624A PHE* 3.2 4.3 - - - -
625A THR* 2.8 55.0 + - - +
627A MET* 3.5 24.6 - - + +
646A PRO* 3.6 21.7 + - - +
647A ASN* 3.6 22.2 + - - +
703A ARG* 3.5 5.6 - - - -
705A THR* 3.3 26.0 - - - +
706A GLY* 4.6 4.7 - - - +
955A ALA 3.7 14.8 + - - -
956A TRP* 3.9 18.8 - - + +
957A ALA 5.1 1.6 + - - -
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Residues in contact with GLU 597 (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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559A TYR* 2.7 35.0 + - + +
595A VAL* 3.7 4.3 + - + -
596A LYS* 1.3 70.1 - - - +
598A SER* 1.3 58.6 + - - +
622A PHE* 4.0 16.2 - - + -
623A SER 3.7 7.9 - - - +
624A PHE* 4.7 0.9 - - + -
676A ILE* 4.8 2.1 - - - +
679A ARG* 3.0 45.2 + - - +
702A PHE* 4.2 5.8 - - + -
703A ARG 3.1 8.0 + - - +
704A GLY* 3.8 16.4 - - - +
705A THR 3.4 4.2 + - - -
706A GLY* 2.7 31.4 + - - -
707A TYR* 3.8 19.0 + - + +
785A ILE* 5.2 0.3 - - - +
786A GLU 5.1 1.0 - - - +
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Residues in contact with SER 598 (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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596A LYS* 4.0 17.7 + - - +
597A GLU* 1.3 78.5 + - - +
599A CYS* 1.3 64.5 + - - +
621A ARG* 3.9 17.3 - - - -
622A PHE* 3.6 8.5 - - - -
623A SER* 2.9 34.8 + - - +
625A THR* 4.5 5.9 + - - -
652A CYS* 5.2 3.1 - - - -
706A GLY* 3.1 20.5 - - - -
707A TYR* 4.6 3.8 - - - -
961A ASN* 4.8 8.1 - - - -
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Residues in contact with CYS 599 (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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598A SER* 1.3 78.0 - - - +
600A ASP* 1.3 69.5 + - - +
620A VAL* 3.6 24.9 - - - -
621A ARG* 3.2 11.9 - - - +
622A PHE* 3.7 18.4 - - + -
668A LEU* 5.1 2.2 - - - -
672A LEU* 4.3 11.7 - - - -
706A GLY 2.8 17.5 + - - +
707A TYR* 3.7 26.5 - - + -
708A ASP 4.8 1.4 + - - -
711A LEU* 3.1 26.5 - - + +
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Residues in contact with ASP 600 (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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599A CYS* 1.3 77.2 - - - +
601A GLY* 1.3 77.2 + - - +
602A MET* 4.1 1.2 + - + +
620A VAL* 3.4 7.0 - - - +
621A ARG* 3.0 52.5 + - - +
662A GLU* 4.5 0.7 - - - +
708A ASP* 3.1 8.0 - - - +
711A LEU* 4.0 6.0 - - - +
961A ASN* 4.5 13.4 - - - +
1102A MN 2.2 35.3 + - - -
32F A 5.4 2.1 + - - -
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Residues in contact with GLY 601 (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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600A ASP* 1.3 97.5 + - - +
602A MET* 1.3 61.1 + - - +
603A GLY 3.4 5.9 + - - -
619A ALA 3.1 10.8 - - - -
620A VAL* 4.4 1.3 - - - -
662A GLU* 3.4 34.2 + - - +
31F T 4.5 3.3 + - - -
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Residues in contact with MET 602 (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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600A ASP* 4.8 1.1 - - + +
601A GLY* 1.3 75.0 - - - +
603A GLY* 1.3 66.5 + - - +
604A ASP 3.3 11.3 + - - +
605A VAL* 4.1 2.9 - - + +
619A ALA* 2.7 30.8 + - + +
620A VAL 5.0 0.2 - - - -
621A ARG* 3.5 49.1 - - + +
657A LEU* 4.7 4.3 - - + -
961A ASN 5.8 2.0 - - - +
964A GLY* 4.0 24.2 - - - +
965A ASN* 3.5 25.6 - - + +
968A PHE* 4.2 33.4 - - + -
991A HIS* 4.9 7.2 - - + -
31F T 3.6 13.2 + - - -
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Residues in contact with GLY 603 (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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601A GLY* 3.4 4.8 + - - -
602A MET* 1.3 80.2 - - - +
604A ASP* 1.3 60.4 + - - -
605A VAL* 4.0 0.2 - - - +
618A LYS* 3.1 50.0 - - - +
619A ALA 3.6 1.5 + - - +
31F T 3.3 14.0 + - - -
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Residues in contact with ASP 604 (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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602A MET 3.3 1.8 + - - +
603A GLY* 1.3 73.0 - - - -
605A VAL* 1.3 73.5 + - - +
606A SER* 2.4 32.7 + - - -
614A ALA* 5.8 3.3 - - - +
616A PRO* 3.4 23.3 - - - +
617A GLU 3.1 10.8 + - - -
618A LYS* 4.1 4.5 - - - +
965A ASN* 3.1 25.1 + - - +
969A ARG* 4.6 7.3 + - - +
30F G 5.2 3.7 - - - +
31F T 4.0 4.4 + - - -
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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
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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