Contacts of the strand formed by residues 635 - 644 (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 ILE 635 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633C PRO 4.0 7.4 - - - +
634C PRO* 1.3 79.7 - - - +
636C ALA* 1.3 69.7 + - + +
637C LEU* 3.1 12.1 - - - +
658C GLU* 3.0 39.8 + - + +
659C ALA 3.7 18.8 - - - +
661C ARG* 3.3 44.6 - - + +
1115D LYS* 6.1 2.7 - - - +
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Residues in contact with ALA 636 (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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635C ILE* 1.3 79.5 - - + +
637C LEU* 1.3 65.7 + - - +
638C ASN* 3.6 10.1 + - - +
656C ARG 3.7 6.5 - - - +
657C TRP* 3.9 4.2 - - - -
658C GLU* 3.2 32.1 - - + +
1599F SER* 5.9 5.2 - - - -
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Residues in contact with LEU 637 (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* 4.3 10.5 - - + +
635C ILE 3.1 21.1 - - - +
636C ALA* 1.3 73.9 - - - +
638C ASN* 1.3 67.9 + - - +
655C VAL* 5.4 2.7 - - + -
656C ARG 3.4 5.8 - - - +
657C TRP* 3.3 18.6 - - + -
710C VAL* 4.5 13.0 - - + +
712C VAL* 3.9 26.2 - - + +
726C SER* 3.2 30.5 - - - +
727C GLU* 4.2 8.5 - - + +
729C LEU* 4.0 22.4 - - + +
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Residues in contact with ASN 638 (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 4.0 9.3 - - - +
637C LEU* 1.3 78.6 - - - +
639C TRP* 1.3 76.9 + - + +
640C THR* 4.7 3.8 + - - -
655C VAL 3.8 0.3 - - - -
656C ARG* 2.8 40.7 + - - +
729C LEU* 3.9 18.1 - - + +
1599F SER* 5.5 7.3 - - - -
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Residues in contact with TRP 639 (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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638C ASN* 1.3 83.9 + - - +
640C THR* 1.3 80.2 + - - +
641C LEU* 3.6 29.4 - - + -
653C ILE* 3.8 32.1 - - + -
654C GLN 3.3 11.0 - - - +
655C VAL* 4.3 8.1 - - + -
729C LEU* 3.7 23.5 - - + +
730C TYR 3.8 13.3 + - - -
731C VAL* 3.7 19.7 - - + +
732C THR* 3.7 27.4 - - - -
733C LEU* 4.0 10.5 - - + -
734C PRO* 4.5 8.7 - - + -
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Residues in contact with THR 640 (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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638C ASN* 4.7 3.6 + - - -
639C TRP* 1.3 84.4 + - - +
641C LEU* 1.3 76.5 + - - +
642C LEU* 5.2 3.1 - - + -
653C ILE* 3.2 1.2 - - - -
654C GLN* 2.7 47.6 + - + +
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Residues in contact with LEU 641 (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* 3.6 24.5 - - + -
640C THR* 1.3 88.6 - - - +
642C LEU* 1.3 72.9 + - - +
643C ASN* 3.6 21.3 - - - +
644C VAL* 3.9 18.4 - - + -
651C ALA* 4.2 12.3 - - + -
652C ASP 3.5 11.4 - - - +
653C ILE* 4.3 4.5 - - + +
733C LEU* 4.9 0.4 - - + -
734C PRO* 3.6 31.0 - - + -
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Residues in contact with LEU 642 (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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350B HIS* 3.8 17.3 - - + +
401B SER* 4.5 11.9 - - - +
640C THR* 5.0 2.5 - - + +
641C LEU* 1.3 80.5 - - - +
643C ASN* 1.3 78.5 + - - +
652C ASP* 2.7 26.9 + - + +
653C ILE 3.1 38.1 - - - +
654C GLN* 3.8 17.7 - - + +
698C PRO* 4.5 4.3 - - + -
700C TYR* 4.0 13.7 - - + -
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Residues in contact with ASN 643 (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* 4.9 1.4 - - - +
349B ILE* 3.5 19.1 - - + +
350B HIS* 2.7 42.0 + - - -
403B LYS* 3.5 14.6 - - - +
641C LEU* 3.6 9.4 - - - +
642C LEU* 1.3 95.2 + - - +
644C VAL* 1.3 66.7 + - - +
645C SER 4.1 0.5 + - - -
651C ALA* 3.9 0.5 - - - -
652C ASP* 3.3 22.9 + - - +
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Residues in contact with VAL 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ILE* 4.0 8.4 - - - +
641C LEU* 3.9 27.4 - - + -
643C ASN* 1.3 77.7 - - - +
645C SER* 1.3 74.1 + - - +
646C LEU* 3.4 2.4 + - - +
648C GLY* 4.0 15.3 - - - +
650C HIS 3.1 24.7 - - - +
651C ALA* 4.0 7.9 - - + +
704C VAL* 4.8 9.9 - - + -
734C PRO* 5.2 8.3 - - + -
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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