Contacts of the strand formed by residues 650 - 658 (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 HIS 650 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346B LEU* 3.9 30.2 + - + +
347B THR* 3.4 19.3 - - + +
644C VAL* 3.1 9.5 - - - +
645C SER* 2.8 31.2 + - - -
647C THR* 5.6 0.2 + - - -
648C GLY 3.3 0.6 + - - -
649C ILE* 1.3 108.8 - - + +
651C ALA* 1.3 61.4 + - - +
701C SER* 3.3 31.9 - - - -
702C LEU 3.2 7.2 - - - +
703C LYS* 2.6 35.5 + - - -
704C VAL* 4.4 1.6 - - - +
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Residues in contact with ALA 651 (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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347B THR* 4.1 1.1 - - - -
641C LEU* 4.2 11.7 - - + -
643C ASN 3.9 6.7 - - - -
644C VAL* 4.0 13.5 - - + -
650C HIS* 1.3 75.1 - - - +
652C ASP* 1.3 69.6 + - - +
653C ILE* 4.8 0.2 - - - -
700C TYR 4.0 0.5 - - - -
701C SER 3.5 0.5 + - - -
702C LEU* 3.1 30.2 + - - +
704C VAL* 4.9 2.2 - - + -
733C LEU* 3.9 35.7 - - + -
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Residues in contact with ASP 652 (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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345B SER* 2.9 27.8 + - - -
347B THR* 3.2 9.2 + - - +
350B HIS* 3.1 22.3 - - + -
641C LEU* 3.5 1.4 - - - +
642C LEU* 2.7 40.2 + - + +
643C ASN 3.3 9.3 + - - +
651C ALA* 1.3 75.4 - - - +
653C ILE* 1.3 65.5 + - - +
699C VAL 3.6 3.4 - - - -
700C TYR* 3.2 20.3 - - + -
701C SER 2.9 27.5 + - - -
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Residues in contact with ILE 653 (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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639C TRP* 3.8 31.4 - - + -
640C THR 3.2 13.2 - - - +
641C LEU* 4.3 3.8 - - + -
642C LEU* 3.1 15.9 - - - +
652C ASP* 1.3 81.9 - - - +
654C GLN* 1.3 63.4 - - - +
655C VAL* 4.2 10.8 - - + -
698C PRO* 3.6 0.7 - - - +
699C VAL* 3.0 42.2 + - + +
702C LEU* 3.7 20.9 - - + -
710C VAL* 5.6 1.6 - - + -
731C VAL* 4.1 18.8 - - + -
733C LEU* 3.6 28.3 - - + -
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Residues in contact with GLN 654 (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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400B TYR* 5.7 3.6 - - - +
401B SER* 4.1 14.9 + - - -
638C ASN 4.1 0.2 - - - +
639C TRP* 3.3 3.3 - - - -
640C THR* 2.7 42.4 + - + +
642C LEU* 4.2 16.8 - - + +
653C ILE* 1.3 76.6 - - - +
655C VAL* 1.3 62.6 + - - +
656C ARG* 3.8 4.9 + - + +
696C SER* 3.1 29.6 + - - +
697C VAL* 3.3 29.0 - - - +
698C PRO* 4.2 4.9 - - - +
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Residues in contact with VAL 655 (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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637C LEU* 5.4 2.7 - - + -
638C ASN 3.8 4.9 - - - +
639C TRP* 4.3 8.3 - - + -
653C ILE* 4.1 14.7 + - + -
654C GLN* 1.3 75.0 + - - +
656C ARG* 1.3 62.8 + - - +
657C TRP* 3.1 30.0 - - + -
676C LEU* 3.6 18.2 - - + -
696C SER* 3.5 1.9 + - - -
697C VAL 3.0 38.5 + - - +
699C VAL* 3.7 19.7 - - + +
710C VAL* 4.4 19.3 - - + -
712C VAL* 5.0 1.8 - - + -
729C LEU* 4.4 9.2 - - + -
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Residues in contact with ARG 656 (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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636C ALA 3.7 1.6 - - - +
637C LEU* 3.4 1.7 - - - +
638C ASN* 2.8 47.4 + - - +
654C GLN* 3.8 5.6 + - + +
655C VAL* 1.3 72.7 - - - +
657C TRP* 1.3 68.2 + - - +
695C THR 3.5 5.4 - - - +
696C SER* 4.0 12.8 - - - +
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Residues in contact with TRP 657 (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* 4.0 18.8 - - + -
636C ALA 3.9 8.1 - - - -
637C LEU* 3.3 24.5 - - + -
655C VAL* 3.1 48.5 - - + -
656C ARG* 1.3 85.5 - - - +
658C GLU* 1.3 61.3 + - - +
674C TYR* 3.6 29.6 - + + -
676C LEU* 4.0 11.9 - - + -
692C ILE* 3.3 28.0 - - + -
694C THR 3.7 1.6 - - - -
695C THR* 2.8 54.4 + - + +
696C SER 4.2 0.2 - - - -
697C VAL* 3.3 29.2 - - + -
712C VAL* 4.1 14.8 - - + +
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Residues in contact with GLU 658 (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* 3.2 9.0 - - - +
635C ILE* 3.0 50.9 + - + +
636C ALA* 3.2 21.4 + - + +
657C TRP* 1.3 78.0 - - - +
659C ALA* 1.3 68.8 + - - +
695C THR* 4.8 0.7 - - - -
1599F SER* 4.8 15.3 + - - +
1600F PHE* 4.9 15.3 - - - -
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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