Contacts of the helix formed by residues 642 - 658 (chain B) in PDB entry 3K5N
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 THR 642 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641B TRP* 1.3 76.5 - - - +
643B PRO* 1.3 69.5 - - + +
644B LEU* 3.3 8.5 - - + +
645B ALA* 2.8 20.3 + - - +
646B GLN* 2.9 14.2 + - - +
681B ARG 2.9 23.6 - - - +
682B LEU* 4.0 12.1 - - - -
683B VAL 3.9 2.3 + - - -
684B TYR* 2.9 36.9 - - - -
752B TYR* 4.3 4.3 - - + -
756B GLN* 1.9 34.2 + - - +
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Residues in contact with PRO 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B TRP 3.9 4.9 - - - +
642B THR* 1.3 83.3 - - + +
644B LEU* 1.3 65.7 + - - +
645B ALA 3.1 0.2 - - - -
646B GLN* 3.4 17.7 - - + +
647B GLN* 2.9 27.5 + - - +
680B ALA 4.9 2.7 - - - +
681B ARG* 3.6 23.5 - - + +
683B VAL* 3.3 22.7 - - + +
685B ARG* 4.8 16.6 - - - +
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Residues in contact with LEU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B THR* 3.1 6.7 + - + -
643B PRO* 1.3 75.9 - - - +
645B ALA* 1.3 57.9 + - - +
647B GLN* 3.9 1.7 - - - +
648B PHE* 2.9 33.3 + - + +
669B THR* 4.9 3.6 - - + -
673B LEU* 4.2 11.9 - - + -
678B LEU* 4.0 27.6 - - + +
681B ARG* 2.9 32.9 + - + +
682B LEU* 3.8 27.8 - - + -
752B TYR* 4.3 9.6 - - + -
756B GLN* 4.3 4.0 - - + +
757B LEU* 2.7 44.0 - - + -
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Residues in contact with ALA 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B GLU* 5.1 2.5 - - + -
636B THR* 5.6 0.4 - - - -
641B TRP* 3.8 22.4 - - + -
642B THR 2.8 12.2 + - - +
644B LEU* 1.3 78.6 - - - +
646B GLN* 1.3 56.4 + - - +
647B GLN 3.1 1.3 - - - -
648B PHE* 4.2 4.7 - - - -
649B GLN* 2.8 36.1 + - - +
756B GLN* 3.6 23.6 - - + +
757B LEU* 5.1 1.6 - - - -
760B VAL* 4.2 15.4 - - + +
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Residues in contact with GLN 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B GLU 2.8 19.5 - - - +
636B THR* 2.5 42.6 + - - +
638B ARG 4.1 10.9 + - - +
639B THR* 5.1 4.6 + - - +
641B TRP* 4.4 14.0 + - - -
642B THR 2.9 17.3 + - - +
643B PRO* 3.4 16.9 + - + +
645B ALA* 1.3 75.2 - - - +
647B GLN* 1.3 58.0 + - - +
650B GLN* 2.8 40.9 + - - +
685B ARG* 5.9 2.4 - - - +
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Residues in contact with GLN 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B PRO 2.9 18.9 + - - +
644B LEU* 3.9 3.6 - - - +
646B GLN* 1.3 78.9 - - - +
648B PHE* 1.3 63.7 + - - +
650B GLN* 3.4 9.8 + - - +
651B GLU* 2.9 59.3 + - + +
681B ARG* 4.0 37.0 + - - +
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Residues in contact with PHE 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B LEU* 2.9 24.7 + - + +
645B ALA* 3.8 2.0 - - - +
647B GLN* 1.3 74.1 - - - +
649B GLN* 1.3 59.0 + - - +
651B GLU* 4.2 0.6 - - - +
652B LEU* 2.9 51.0 + - + +
665B TYR* 3.9 26.0 + + - +
666B VAL* 4.1 42.4 - - + -
669B THR* 4.5 15.3 - - + -
670B ILE* 5.8 0.7 - - + -
757B LEU* 3.3 44.0 - - + -
758B GLN* 6.0 1.1 - - - -
760B VAL* 3.7 26.7 - - + -
761B ALA* 4.3 6.5 - - + -
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Residues in contact with GLN 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B PHE* 4.2 8.1 - - + -
634B LEU* 3.4 13.7 - - - +
635B GLU* 2.7 39.7 + - - +
636B THR* 2.5 44.7 + - - +
645B ALA 2.8 22.6 + - - +
646B GLN 3.9 1.1 - - - +
648B PHE* 1.3 75.1 - - - +
650B GLN* 1.3 62.0 + - - +
652B LEU* 4.4 0.4 - - - -
653B TYR* 2.8 59.3 + - + -
760B VAL* 4.1 20.5 + - + +
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Residues in contact with GLN 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B MET* 4.0 5.6 - - - +
631B PHE* 4.4 17.7 - - + -
636B THR* 3.1 25.3 + - - +
646B GLN* 2.8 29.4 + - - +
647B GLN* 3.7 10.3 - - - +
649B GLN* 1.3 78.0 - - - +
651B GLU* 1.3 64.5 + - + +
653B TYR* 3.8 2.1 - - - +
654B LEU* 3.2 24.2 + - - +
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Residues in contact with GLU 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B GLN* 2.9 45.7 + - + +
650B GLN* 1.3 76.6 - - + +
652B LEU* 1.3 61.4 + - - +
654B LEU* 3.5 7.1 + - - +
655B ARG* 3.0 33.1 + - + +
665B TYR* 2.3 43.7 + - + +
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Residues in contact with LEU 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B PHE* 2.9 52.8 + - + +
649B GLN 3.7 2.9 - - - +
651B GLU* 1.3 76.7 - - - +
653B TYR* 1.3 67.1 + - + +
655B ARG* 3.3 3.0 + - - +
656B ILE* 3.1 36.0 + - + +
662B TYR* 4.1 26.7 - - + -
665B TYR* 4.3 9.2 - - + -
666B VAL* 4.8 5.6 - - + -
760B VAL* 4.5 8.7 - - + -
761B ALA* 4.5 7.6 - - + -
764B ILE* 4.0 21.3 - - + -
765B LEU* 4.7 7.0 - - + -
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Residues in contact with TYR 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B LEU* 3.5 30.5 - - + +
618B ALA* 3.8 15.3 - - + -
629B MET* 3.8 14.1 - - + -
631B PHE* 3.7 16.8 - + + -
634B LEU* 3.7 17.5 - - - +
649B GLN* 2.8 56.4 + - + +
650B GLN 3.8 1.8 - - - +
652B LEU* 1.3 78.6 - - + +
654B LEU* 1.3 54.5 + - - +
656B ILE* 2.9 4.7 + - - +
657B PHE* 2.7 59.2 + + + -
760B VAL* 4.8 10.1 + - + -
763B GLY* 5.1 1.9 - - - -
764B ILE* 4.1 34.4 + - + +
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Residues in contact with LEU 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B LEU* 4.0 24.5 - - + -
627B GLN* 4.8 4.7 - - + +
629B MET* 3.9 17.0 - - + -
650B GLN 3.2 16.1 + - - +
651B GLU* 3.7 7.4 - - - +
653B TYR* 1.3 81.4 - - - +
655B ARG* 1.3 57.1 + - + +
657B PHE* 4.4 2.0 - - + -
658B ARG* 2.7 61.6 + - + +
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Residues in contact with ARG 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B GLU* 3.0 25.6 + - + +
652B LEU* 3.5 7.2 - - - +
654B LEU* 1.3 77.3 - - - +
656B ILE* 1.3 62.6 + - - +
658B ARG 3.3 0.3 + - - -
659B ASN 3.1 2.4 + - - -
660B GLU* 2.7 50.0 + - - +
661B PRO* 1.9 49.7 + - - +
662B TYR* 3.7 21.1 - - + +
665B TYR* 3.8 38.5 - - - +
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Residues in contact with ILE 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B LEU* 4.9 11.7 - - + -
600B ARG* 4.0 4.2 + - - +
652B LEU* 3.3 29.2 - - + +
653B TYR 2.9 5.9 + - - +
655B ARG* 1.3 75.3 - - + +
657B PHE* 1.3 61.2 + - + +
658B ARG 2.9 1.6 - - - -
659B ASN* 2.5 33.9 + - - +
660B GLU 4.4 3.8 - - - -
662B TYR* 4.2 17.5 - - + -
764B ILE* 3.1 33.7 - - + -
765B LEU* 4.0 18.4 - - + -
768B ILE* 4.3 23.1 - - + -
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Residues in contact with PHE 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU* 3.9 26.7 - - + -
600B ARG* 2.3 58.3 + - + +
602B LEU* 4.0 18.2 - - + -
618B ALA 4.5 0.2 - - - -
619B GLY* 4.0 21.1 - - - -
620B LEU* 3.9 28.4 - - + +
629B MET* 3.0 38.6 - - + -
653B TYR* 2.7 44.4 + + + +
654B LEU* 4.1 4.3 - - - +
656B ILE* 1.3 74.0 - - + +
658B ARG* 1.3 59.3 + - - +
659B ASN 3.2 1.9 + - - -
764B ILE* 5.3 2.5 - - + -
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Residues in contact with ARG 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B LEU* 4.9 2.2 - - + -
627B GLN* 2.0 49.8 + - - +
654B LEU* 2.7 47.5 + - + +
655B ARG 3.8 3.6 - - - +
656B ILE 2.9 0.6 - - - -
657B PHE* 1.3 77.7 - - + +
659B ASN* 1.3 73.7 + - - +
660B GLU* 3.0 34.6 + - - +
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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
------------------------------------------------------------
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