Contacts of the helix formed by residues 655 - 675 (chain A) in PDB entry 6S1M
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 655 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A MET* 4.1 15.9 - - + -
559A LEU* 4.0 28.7 - - + +
562A GLN* 4.6 18.6 - - + +
563A ALA* 4.6 16.8 - - + +
566A GLU* 4.4 19.3 - - + +
568A LEU* 4.1 24.5 - - + -
617A CYS* 3.3 8.5 - - - -
619A THR* 3.9 14.4 - - + +
653A LYS 4.7 3.6 - - - +
654A GLY* 1.3 77.5 - - - +
656A LEU* 1.3 64.8 + - - +
657A PRO 3.5 0.4 - - - -
658A GLN* 3.4 12.8 + - - +
659A ILE* 3.2 28.0 + - + +
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Residues in contact with LEU 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A VAL* 5.9 4.0 - - + -
559A LEU* 4.1 24.5 - - + -
611A MET* 3.9 28.3 - - + -
616A LEU 4.5 0.4 - - - +
617A CYS* 4.2 19.1 - - - -
618A TYR* 4.3 25.6 - - + +
655A LEU* 1.3 75.7 - - - +
657A PRO* 1.4 70.9 - - + +
659A ILE* 4.1 12.2 - - + +
660A LEU* 3.0 33.9 + - + +
700A VAL* 4.9 17.0 - - + +
703A PHE* 6.6 0.2 - - + -
704A THR* 4.7 10.1 - - - +
716A ILE* 5.3 3.1 - - + -
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Residues in contact with PRO 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A MET* 3.8 20.0 - - + +
612A MET* 4.2 26.1 - - + +
615A ASN* 4.7 8.3 - - - +
616A LEU 3.7 14.8 - - - +
617A CYS* 4.6 0.4 - - + -
653A LYS* 4.8 10.1 - - + -
654A GLY* 3.9 22.2 - - - +
655A LEU 3.9 1.1 - - - -
656A LEU* 1.4 91.3 - - + +
658A GLN* 1.3 59.4 + - + +
660A LEU* 3.5 2.3 + - + +
661A GLU* 2.9 35.7 + - - +
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Residues in contact with GLN 658 (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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562A GLN* 4.4 26.4 + - - +
566A GLU* 4.4 15.0 + - - -
653A LYS* 4.2 26.3 + - + +
654A GLY 3.5 23.0 + - - +
655A LEU* 3.4 11.8 + - - +
656A LEU 3.3 0.8 - - - -
657A PRO* 1.3 74.9 - - + +
659A ILE* 1.3 67.1 + - - +
661A GLU* 3.3 7.8 + - - +
662A ASN* 3.1 23.0 + - - +
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Residues in contact with ILE 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A VAL* 5.3 5.4 - - + +
558A GLN* 3.3 36.3 - - + +
559A LEU* 3.9 42.2 - - + +
562A GLN* 3.8 22.9 - - + +
655A LEU 3.2 18.5 + - - +
656A LEU* 4.1 14.1 - - + +
657A PRO 3.5 0.2 - - - -
658A GLN* 1.3 76.0 - - - +
660A LEU* 1.3 62.1 + - + +
662A ASN* 3.4 10.1 + - - +
663A LEU* 3.1 28.6 + - + +
700A VAL* 5.0 9.9 - - + -
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Residues in contact with LEU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A PRO* 3.9 37.6 - - + +
611A MET* 4.0 24.2 - - + -
612A MET* 3.7 13.4 - - + +
656A LEU* 3.0 24.0 + - + +
657A PRO* 3.8 3.8 - - + +
659A ILE* 1.3 77.8 - - - +
661A GLU* 1.3 56.7 + - - +
663A LEU* 3.3 4.5 + - + +
664A LEU* 2.9 30.1 + - - +
697A ALA* 3.5 37.0 - - + +
700A VAL* 3.8 24.9 - - + -
701A TYR* 5.9 1.6 - - + +
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Residues in contact with GLU 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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612A MET* 3.7 27.0 - - + +
657A PRO* 2.9 20.7 + - - +
658A GLN* 3.3 8.3 + - - +
660A LEU* 1.3 74.6 - - - +
662A ASN* 1.3 63.2 + - - +
664A LEU* 3.4 9.3 + - + +
665A SER* 3.0 24.3 + - - -
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Residues in contact with ASN 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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538A VAL* 4.5 25.8 + - - +
558A GLN* 5.4 4.6 - - - +
562A GLN* 5.9 4.4 - - - +
658A GLN 3.1 12.9 + - - +
659A ILE* 3.7 12.7 + - - +
661A GLU* 1.3 76.0 - - - +
663A LEU* 1.3 64.5 + - - +
665A SER* 3.4 6.6 + - - -
666A ALA* 3.1 22.2 + - - +
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Residues in contact with LEU 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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535A MET* 5.3 2.7 - - + -
538A VAL* 4.4 19.5 - - + -
539A THR* 5.7 0.2 - - + -
558A GLN* 4.3 21.5 - - - +
659A ILE* 3.1 21.1 + - + +
660A LEU* 3.8 6.1 - - + +
662A ASN* 1.3 79.3 - - - +
664A LEU* 1.3 57.5 + - - +
666A ALA* 3.3 5.4 + - - +
667A ARG* 3.1 28.8 + - - +
693A LEU* 4.4 17.7 - - + +
696A SER* 4.1 21.3 - - - -
697A ALA* 4.0 32.8 - - + +
700A VAL* 4.1 18.6 - - + -
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Residues in contact with LEU 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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605A SER* 4.5 23.6 - - - +
608A PRO* 5.3 4.9 - - + -
609A SER* 4.8 7.4 - - - +
612A MET* 3.8 24.2 - - + -
660A LEU 2.9 15.4 + - - +
661A GLU* 3.7 11.0 - - + +
662A ASN 3.2 0.2 - - - -
663A LEU* 1.3 74.7 - - - +
665A SER* 1.3 62.4 + - - +
667A ARG* 3.4 6.2 + - - +
668A LYS* 3.0 39.4 + - + +
697A ALA* 5.6 4.0 - - + +
789A PRO* 5.7 7.2 - - + -
791A ARG* 6.3 1.8 - - - +
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Residues in contact with SER 665 (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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661A GLU 3.0 16.6 + - - -
662A ASN* 3.9 5.6 - - - -
663A LEU 3.4 0.2 - - - -
664A LEU* 1.3 81.2 - - - +
666A ALA* 1.3 55.7 + - - +
668A LYS* 3.3 8.8 + - - +
669A ARG* 3.0 43.2 + - - +
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Residues in contact with ALA 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A GLU* 5.4 2.8 - - - +
538A VAL* 4.7 17.9 - - + -
662A ASN* 3.1 16.0 + - - +
663A LEU* 3.6 10.1 - - - +
664A LEU 3.3 0.2 - - - -
665A SER* 1.3 76.6 - - - +
667A ARG* 1.3 61.6 + - - +
669A ARG* 3.4 27.5 + - - +
670A ALA* 3.1 22.0 + - - +
689A ARG* 5.6 1.0 + - - -
693A LEU* 4.0 19.5 - - + +
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Residues in contact with ARG 667 (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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605A SER* 3.9 16.2 + - - -
663A LEU 3.1 16.2 + - - +
664A LEU* 3.9 5.8 - - - +
666A ALA* 1.3 76.8 - - - +
668A LYS* 1.3 57.9 + - - +
670A ALA* 3.2 2.5 + - - +
671A LYS* 3.0 51.6 + - + +
690A GLN* 2.8 54.7 + - + +
693A LEU* 3.9 22.6 - - + +
694A LYS* 3.5 33.9 - - - +
101T TTP 3.1 32.3 + - - -
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Residues in contact with LYS 668 (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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664A LEU* 3.0 28.9 + - + +
665A SER* 3.6 8.5 - - - +
667A ARG* 1.3 78.3 - - - +
669A ARG* 1.3 56.8 + - + +
671A LYS* 3.4 11.0 + - + +
672A ALA* 2.9 29.5 + - + +
791A ARG* 4.5 18.6 - - - +
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Residues in contact with ARG 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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305A GLN* 5.6 5.9 - - - +
534A GLU* 5.6 5.7 + - - +
538A VAL* 5.6 6.3 - - - +
665A SER* 3.0 25.0 + - - +
666A ALA* 3.7 27.8 + - - +
668A LYS* 1.3 73.8 - - + +
670A ALA* 1.3 60.2 + - - +
672A ALA* 3.7 7.4 - - + +
673A GLU* 3.0 28.9 + - - +
689A ARG* 5.4 7.2 - - - +
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Residues in contact with ALA 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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666A ALA 3.1 14.2 + - - +
667A ARG* 3.2 8.0 + - - +
669A ARG* 1.3 77.7 - - - +
671A LYS* 1.3 56.4 + - - +
673A GLU* 3.4 6.6 + - - +
674A LEU* 2.9 28.0 + - - +
686A LEU* 5.3 1.9 - - - +
689A ARG* 3.7 35.7 + - + +
690A GLN* 4.3 15.3 - - + +
693A LEU* 4.2 14.4 - - + -
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Residues in contact with LYS 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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667A ARG* 3.0 62.9 + - - +
668A LYS* 3.8 9.0 - - + +
669A ARG 3.3 0.2 - - - -
670A ALA* 1.3 74.1 - - - +
672A ALA* 1.3 60.4 + - - +
674A LEU* 3.0 12.9 + - + +
675A ALA* 3.0 29.8 + - - +
690A GLN* 4.2 22.0 + - + +
101T TTP 4.5 4.4 + - - -
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Residues in contact with ALA 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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668A LYS* 2.9 18.1 + - + +
669A ARG* 3.7 8.5 - - + +
671A LYS* 1.3 75.9 - - - +
673A GLU* 1.3 61.4 + - - +
675A ALA* 3.7 14.4 + - - +
676A LYS* 4.5 6.2 - - - +
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Residues in contact with GLU 673 (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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669A ARG 3.0 17.1 + - - +
670A ALA* 3.7 5.4 - - - +
672A ALA* 1.3 77.8 - - - +
674A LEU* 1.3 61.6 + - - +
676A LYS* 3.3 41.9 + - - +
677A GLU* 4.5 5.0 - - - +
686A LEU* 3.3 36.4 - - - +
689A ARG* 3.4 23.1 + - - +
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Residues in contact with LEU 674 (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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670A ALA 2.9 15.0 + - - +
671A LYS* 3.0 14.5 + - + +
673A GLU* 1.3 73.4 + - - +
675A ALA* 1.3 56.8 + - - +
676A LYS 3.0 11.1 + - - -
677A GLU* 3.6 11.0 + - - +
683A ARG* 3.3 52.1 + - + +
686A LEU* 3.7 28.0 - - + +
687A ASP* 4.0 26.0 - - + +
690A GLN* 4.1 14.8 - - + +
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Residues in contact with ALA 675 (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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671A LYS 3.0 13.8 + - - +
672A ALA* 4.0 10.8 - - - +
673A GLU 3.2 1.6 - - - -
674A LEU* 1.3 75.4 - - - +
676A LYS* 1.3 58.9 + - - +
677A GLU 3.8 0.9 - - - -
683A ARG* 5.2 10.0 + - - +
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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
------------------------------------------------------------
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