Contacts of the strand formed by residues 672 - 680 (chain C) in PDB entry 1KF9
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 672 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631C PRO* 3.9 11.0 - - + -
659C ALA* 4.8 1.8 - - + -
660C PRO* 4.1 15.0 - - + -
663C ALA* 3.7 29.4 - - + -
670C MET* 4.1 22.4 + - + +
671C VAL* 1.3 79.6 - - - +
673C GLU* 1.3 60.1 + - - +
674C TYR* 3.7 26.2 - - + +
693C LEU* 4.0 20.4 - - - +
714C SER* 4.0 15.3 - - - +
715C LYS 3.2 26.9 - - - +
716C GLN* 3.5 9.0 - - - +
717C ARG* 5.1 0.9 - - - -
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Residues in contact with GLU 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672C LEU* 1.3 74.3 - - - +
674C TYR* 1.3 68.3 + - - +
691C PRO* 4.2 22.2 - - + +
692C ILE 3.3 13.5 - - - +
693C LEU* 4.3 16.3 - - + +
714C SER* 3.7 1.9 - - - -
715C LYS* 3.4 56.9 + - + +
717C ARG* 3.8 23.2 - - + +
718C ASN 4.4 2.9 + - - -
722C TYR* 4.2 7.6 + - - +
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Residues in contact with TYR 674 (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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634C PRO* 4.1 18.8 - - + -
657C TRP* 3.6 28.5 - + + +
659C ALA* 3.2 27.5 - - - +
660C PRO* 4.4 7.2 - - + -
672C LEU* 3.7 28.9 - - + +
673C GLU* 1.3 76.6 - - - +
675C GLU* 1.3 62.6 + - - +
676C LEU 4.0 0.5 + - - -
690C ASP 4.6 0.2 - - - +
691C PRO* 3.4 4.8 - - - +
692C ILE* 2.8 43.5 + - + +
693C LEU 4.7 4.0 - - - -
694C THR 3.6 22.9 - - - -
695C THR* 4.1 15.5 - - + +
712C VAL* 3.7 10.1 - - + -
713C ARG 3.5 4.9 - - - +
714C SER* 3.5 25.6 - - - -
722C TYR* 4.3 1.1 - - - -
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Residues in contact with GLU 675 (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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674C TYR* 1.3 73.1 - - - +
676C LEU* 1.3 61.2 + - - +
677C GLN* 3.3 11.8 + - + +
688C MET* 3.3 31.7 - - - +
689C MET 4.3 12.8 - - - +
690C ASP 5.7 0.2 - - - -
691C PRO* 4.6 5.6 - - + +
712C VAL* 3.2 4.3 - - - +
713C ARG* 2.7 72.8 + - + +
722C TYR* 3.1 37.2 + - + +
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Residues in contact with LEU 676 (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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655C VAL* 3.6 29.8 - - + -
657C TRP* 4.0 13.2 - - + -
674C TYR 4.0 2.2 + - - -
675C GLU* 1.3 74.6 - - - +
677C GLN* 1.3 68.6 + - - +
678C TYR* 3.6 28.0 - - + -
687C LYS 3.7 0.3 - - - +
688C MET* 3.8 1.0 - - - -
689C MET* 3.1 52.2 + - + +
692C ILE* 5.8 1.1 - - + +
697C VAL* 4.0 7.9 - - + -
699C VAL* 4.7 4.7 - - + -
710C VAL* 3.4 26.9 - - + -
711C ARG 3.7 3.4 - - - -
712C VAL* 3.6 12.6 - - + -
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Residues in contact with GLN 677 (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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675C GLU* 3.3 11.6 + - + -
676C LEU* 1.3 80.1 - - - +
678C TYR* 1.3 63.6 + - - +
686C TRP* 3.3 18.7 - - + +
687C LYS 3.1 8.3 - - - +
688C MET* 3.3 22.1 - - + +
710C VAL* 3.4 4.0 - - - +
711C ARG* 2.8 62.4 + - - +
713C ARG* 2.9 31.5 - - - +
725C PHE* 3.2 24.3 - - + -
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Residues in contact with TYR 678 (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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676C LEU* 3.6 17.5 - - + -
677C GLN* 1.3 77.0 - - - +
679C LYS* 1.3 63.8 + - - +
686C TRP* 3.4 3.8 - - - -
687C LYS* 2.9 75.9 + - + +
689C MET* 4.2 17.4 - - + -
699C VAL* 3.7 28.0 - - + +
700C TYR 4.6 8.3 + - - -
702C LEU* 4.0 13.0 - - + -
708C TYR* 4.1 16.4 - + + -
709C GLU 3.2 13.7 - - - +
710C VAL* 3.8 17.0 - - + -
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Residues in contact with LYS 679 (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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678C TYR* 1.3 79.6 - - - +
680C GLU* 1.3 75.3 + - - +
681C VAL 2.7 22.8 + - - -
683C GLU* 3.2 29.1 + - + +
684C THR 4.7 2.9 - - - -
685C LYS 3.6 21.5 - - - +
686C TRP* 3.5 49.8 - - + +
687C LYS* 4.8 2.0 - - - +
708C TYR* 3.4 5.7 - - - -
709C GLU* 2.6 52.1 + - + +
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Residues in contact with GLU 680 (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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679C LYS* 1.3 79.3 + - - +
681C VAL* 1.3 69.1 + - - +
682C ASN 3.0 3.6 - - - +
683C GLU* 2.8 42.9 + - + +
706C LYS* 3.7 28.3 - - + +
707C GLU 3.4 11.7 - - - +
708C TYR* 3.6 20.8 - - + +
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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