Contacts of the strand formed by residues 618 - 633 (chain C) 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 LYS 618 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603C GLY* 3.1 32.2 - - - +
604C ASP* 4.2 5.6 - - - +
616C PRO* 4.1 14.6 + - + +
617C GLU* 1.3 79.0 - - - +
619C ALA* 1.3 62.0 + - - +
659C LEU* 3.2 12.7 - - - +
660C ALA* 3.1 34.1 + - - +
661C ASP* 3.1 34.5 - - + +
662C GLU 5.5 0.9 - - - +
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Residues in contact with ALA 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601C GLY* 3.3 3.1 - - - -
602C MET* 2.6 56.5 + - + +
603C GLY 3.7 4.9 + - - -
605C VAL* 3.8 17.5 - - + -
618C LYS* 1.3 79.1 - - - +
620C VAL* 1.3 60.1 + - - +
658C MET 3.0 15.3 - - - +
659C LEU* 3.8 10.5 - - + -
660C ALA 3.7 1.8 - - - -
968C PHE* 4.5 4.0 - - + -
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Residues in contact with VAL 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599C CYS* 3.9 22.2 - - - -
600C ASP 3.5 15.9 - - - +
601C GLY 4.5 0.7 - - - +
602C MET* 4.3 1.8 - - - +
619C ALA* 1.3 75.3 - - - +
621C ARG* 1.3 65.1 + - - +
622C PHE 4.2 0.9 - - - +
656C CYS 4.0 0.5 - - - +
657C LEU* 3.7 4.7 - - - +
658C MET* 2.9 59.7 + - + +
660C ALA* 3.2 23.3 - - + +
661C ASP 4.3 1.1 - - - +
662C GLU* 4.1 23.1 - - + +
668C LEU* 4.4 15.0 - - + -
711C LEU* 5.4 1.1 - - + -
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Residues in contact with ARG 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598C SER* 3.9 14.8 + - - -
599C CYS* 3.5 6.3 - - - -
600C ASP* 3.0 49.4 + - - +
602C MET* 3.9 22.7 - - - +
620C VAL* 1.3 74.0 - - - +
622C PHE* 1.3 60.5 + - - +
623C SER* 3.1 31.5 + - - +
652C CYS* 4.5 12.5 - - - -
654C PRO* 5.1 3.6 - - + -
656C CYS 3.6 3.4 - - - +
657C LEU* 3.3 25.1 - - + -
961C ASN* 3.8 37.8 + - - +
964C GLY* 4.4 11.5 - - - -
991C HIS* 4.6 18.3 - - + -
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Residues in contact with PHE 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559C TYR* 4.1 9.9 - + - -
597C GLU* 3.1 29.2 - - + -
598C SER 3.6 13.5 - - - -
599C CYS* 3.9 17.3 - - + -
620C VAL* 4.2 0.8 - - - +
621C ARG* 1.3 71.4 - - - +
623C SER* 1.3 55.0 + - - +
654C PRO* 4.2 0.3 - - - +
655C LEU* 2.8 48.8 + - + +
656C CYS* 2.9 24.6 + - + +
658C MET* 5.5 1.5 - - + +
672C LEU* 3.9 25.8 - - + -
675C LEU* 3.4 30.7 - - + -
676C ILE* 4.4 14.4 - - + -
707C TYR* 3.4 22.4 - - - -
785C ILE* 4.9 4.0 - - + -
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Residues in contact with SER 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C GLU* 3.9 4.9 - - - +
598C SER* 3.0 38.1 + - - +
621C ARG* 3.1 29.5 + - - -
622C PHE* 1.3 77.1 - - - +
624C PHE* 1.3 64.9 + - - +
652C CYS* 3.3 23.7 - - - -
653C LYS 3.3 17.0 - - - -
654C PRO* 4.0 4.7 - - - -
655C LEU* 3.9 5.2 - - - +
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Residues in contact with PHE 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559C TYR* 4.1 16.8 - + - +
562C ALA* 3.8 33.7 - - + -
563C LEU* 4.0 17.9 - - + -
566C ALA* 3.9 28.0 - - + -
595C VAL* 3.9 21.5 - - + -
596C LYS 3.4 11.7 - - - +
597C GLU* 4.6 0.4 - - - -
598C SER* 4.8 1.3 - - - +
623C SER* 1.3 76.0 - - - +
625C THR* 1.3 68.0 + - - +
626C VAL* 4.0 9.0 - - + -
652C CYS* 4.6 1.1 - - - -
653C LYS* 2.7 65.0 + - + +
655C LEU* 3.7 23.6 - - + -
992C TRP* 4.2 3.6 - + - -
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Residues in contact with THR 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595C VAL* 3.5 2.3 - - - -
596C LYS* 2.9 56.7 + - - -
598C SER* 5.8 2.1 - - - -
624C PHE* 1.3 80.3 + - - +
626C VAL* 1.3 71.5 + - - +
627C MET* 3.2 24.7 + - - +
643C GLU* 5.0 1.3 - - + -
646C PRO* 4.1 16.0 + - + +
651C CYS* 3.6 25.7 + - + +
652C CYS* 3.7 14.2 - - - +
653C LYS* 5.7 0.2 - - - -
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Residues in contact with VAL 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C LEU* 5.0 0.4 - - + -
566C ALA* 4.5 13.9 - - + -
567C LEU* 4.5 11.9 - - + -
570C MET* 4.0 30.7 - - + +
593C VAL* 3.7 25.8 - - + -
594C VAL 3.8 3.4 - - - +
595C VAL* 4.7 4.9 - - + +
624C PHE* 4.0 22.6 - - + -
625C THR* 1.3 74.7 - - - +
627C MET* 1.3 60.0 - - - +
628C ARG 4.3 0.7 - - - +
629C ILE* 4.0 11.4 - - + -
641C PHE* 3.9 9.8 - - + -
643C GLU* 3.7 18.0 - - - +
651C CYS* 4.7 2.5 + - - +
653C LYS* 5.9 2.4 - - + +
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Residues in contact with MET 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594C VAL* 2.8 24.5 + - + +
596C LYS* 3.5 33.7 - - + +
625C THR* 3.6 22.4 - - - +
626C VAL* 1.3 73.3 - - - +
628C ARG* 1.3 70.3 + - + +
641C PHE* 5.1 0.2 - - - -
642C GLU* 3.6 6.5 - - - +
643C GLU* 3.5 22.7 + - + +
646C PRO* 3.7 33.4 - - + -
955C ALA* 4.1 14.6 - - + +
956C TRP* 4.2 26.5 - - + -
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Residues in contact with ARG 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592C THR 3.7 1.1 - - - +
593C VAL* 3.5 2.6 - - - +
594C VAL* 2.8 62.6 + - + +
626C VAL* 3.6 2.8 - - - +
627C MET* 1.3 87.7 + - - +
629C ILE* 1.3 65.3 + - - +
630C THR* 4.2 17.1 - - + +
639C LYS* 3.4 34.8 - - - +
641C PHE* 3.3 15.7 - - - +
642C GLU* 3.9 14.6 + - + +
703C ARG* 5.9 1.2 - - - +
950C ASP 5.7 1.8 + - - -
956C TRP* 5.1 15.6 - - - -
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Residues in contact with ILE 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567C LEU* 4.6 6.1 - - + -
570C MET* 3.9 20.2 - - - -
574C ILE* 3.7 35.2 - - + -
591C PHE* 4.3 28.7 - - + -
592C THR 3.3 8.3 - - - +
593C VAL* 3.8 27.6 - - + -
626C VAL* 4.0 2.2 - - + -
628C ARG* 1.3 79.0 - - - +
630C THR* 1.3 56.3 + - - +
639C LYS* 3.7 0.5 - - - -
640C VAL* 2.8 33.2 + - + +
641C PHE* 2.9 30.3 + - + +
698C PHE* 5.0 1.3 - - + -
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Residues in contact with THR 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590C PRO 4.1 0.3 - - - +
591C PHE* 3.2 7.8 - - - +
592C THR* 2.8 52.5 + - + +
594C VAL* 6.3 2.2 - - + -
628C ARG* 4.3 19.1 - - + +
629C ILE* 1.3 76.5 - - - +
631C ILE* 1.3 61.8 + - - +
637C ASN* 4.6 21.5 + - + +
638C VAL 3.4 11.4 - - - -
639C LYS* 4.0 19.1 - - + +
640C VAL* 4.9 0.7 - - - -
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Residues in contact with ILE 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C MET* 3.7 20.0 - - + -
583C LEU* 3.6 13.9 - - + -
587C LEU* 4.0 18.6 - - + -
589C GLY 3.6 21.5 - - - +
590C PRO 4.2 1.6 - - - -
591C PHE* 3.5 36.6 - - + -
630C THR* 1.3 75.0 - - - +
632C GLU* 1.3 68.2 + - - +
637C ASN* 3.6 4.9 - - - -
638C VAL* 2.9 51.5 + - + +
640C VAL* 3.8 12.4 - - + +
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Residues in contact with GLU 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589C GLY* 4.8 8.5 - - - -
590C PRO* 3.8 28.3 + - + +
631C ILE* 1.3 84.2 - - - +
633C HIS* 1.3 58.4 + - - +
634C GLY 4.1 9.0 + - - +
635C SER* 6.2 0.4 - - - -
636C GLN 3.6 7.4 - - - +
637C ASN* 3.8 16.4 - - - +
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Residues in contact with HIS 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583C LEU* 4.2 28.0 - - + -
587C LEU* 5.4 5.4 - - + -
631C ILE 3.8 2.6 + - - -
632C GLU* 1.3 71.7 - - - +
634C GLY* 1.3 65.7 + - - +
635C SER 3.1 0.2 + - - -
636C GLN* 3.1 29.1 + - + +
638C VAL* 4.8 3.6 - - + -
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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
------------------------------------------------------------
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