Contacts of the helix formed by residues 641 - 653 (chain B) in PDB entry 1QXP
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 PRO 641 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514B ASP* 3.8 13.7 - - + +
515B ASP 4.8 7.0 - - - +
517B ILE* 3.7 23.1 - - + +
640B LEU* 1.3 92.4 - - + +
642B CYS* 1.3 67.8 + - - +
643B GLN* 2.8 23.3 + - + +
644B LEU* 3.3 15.7 + - + +
645B HIS* 3.6 4.1 + - - -
884B GLN* 3.3 36.3 - - - +
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Residues in contact with CYS 642 (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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370B THR* 3.5 26.5 - - + -
383B VAL 5.0 2.2 - - - +
384B ASN 4.7 0.4 - - - -
385B PRO* 4.4 18.2 - - + -
448B HIS* 3.8 19.7 - - - -
514B ASP* 3.2 28.4 + - - -
630B ARG* 4.1 6.1 - - - +
640B LEU 3.7 0.8 + - - -
641B PRO* 1.3 67.7 - - - +
643B GLN* 1.3 68.0 + - - +
645B HIS* 2.7 27.0 + - + -
646B GLN* 3.0 11.1 + - - +
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Residues in contact with GLN 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B PRO* 2.8 18.1 + - + +
642B CYS* 1.3 80.6 - - - +
644B LEU* 1.3 56.2 + - + +
646B GLN* 3.1 35.6 + - - +
647B VAL* 3.5 11.0 + - - +
780B THR* 5.4 1.4 + - - +
884B GLN* 3.0 43.4 + - - +
888B GLN* 3.7 24.2 + - - +
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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
----------------------------------------------------------
517B ILE* 4.4 4.5 - - + -
640B LEU* 3.5 40.8 - - + -
641B PRO* 3.3 12.2 + - + -
642B CYS 3.1 0.4 + - - -
643B GLN* 1.3 68.7 - - + +
645B HIS* 1.3 56.2 + - - +
646B GLN 2.9 4.5 - - - -
647B VAL* 3.1 17.9 - - + +
648B ILE* 2.9 35.3 + - + +
671B LEU* 5.5 0.9 - - + -
884B GLN* 3.6 27.6 - - - +
887B LEU* 3.5 46.0 - - + +
888B GLN* 4.1 9.2 - - + +
891B MET* 4.5 7.6 - - + -
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Residues in contact with HIS 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B SER* 3.5 13.2 - - - +
629B MET* 6.5 0.4 - - + -
630B ARG* 2.9 88.1 + - + +
633B ILE* 4.2 14.4 - - + +
634B GLU* 5.9 2.7 - - + -
639B LYS* 6.2 0.2 - - - -
640B LEU* 3.5 29.3 + - + +
641B PRO 3.6 22.2 - - - -
642B CYS* 2.7 16.0 + - + +
644B LEU* 1.3 70.3 - - - +
646B GLN* 1.3 66.2 + - - +
648B ILE* 3.6 6.2 - - + +
649B VAL* 3.3 26.1 + - + +
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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
----------------------------------------------------------
364B THR* 1.9 40.7 + - - +
366B ARG* 3.1 15.0 - - + +
369B SER* 3.0 23.6 - - - +
370B THR* 2.7 33.4 + - + +
642B CYS* 3.0 8.6 + - - +
643B GLN* 3.1 28.5 + - - +
645B HIS* 1.3 84.0 - - - +
647B VAL* 1.3 67.6 + - - +
648B ILE 2.7 2.9 + - - -
649B VAL* 3.5 0.4 - - - -
650B ALA* 2.8 24.1 + - + -
780B THR* 4.0 16.6 + - - +
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Residues in contact with VAL 647 (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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4B ILE* 4.9 0.2 - - + -
643B GLN 4.1 5.2 - - - +
644B LEU* 3.1 44.2 - - + +
646B GLN* 1.3 73.9 - - - +
648B ILE* 1.3 49.5 + - + +
650B ALA* 4.3 6.7 - - - -
651B ARG* 2.8 34.9 + - - +
780B THR* 3.9 22.4 - - + -
888B GLN* 4.5 18.6 - - + +
891B MET* 4.2 10.5 - - + +
892B TYR* 3.6 36.5 - - + +
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Residues in contact with ILE 648 (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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629B MET* 4.0 15.0 - - + -
633B ILE* 3.3 35.9 - - + -
640B LEU* 3.5 24.5 - - + -
644B LEU* 2.9 26.1 + - + +
645B HIS* 3.6 10.3 - - + +
646B GLN 2.7 2.8 + - - -
647B VAL* 1.3 72.0 - - + +
649B VAL* 1.3 69.3 + - + +
651B ARG* 3.6 0.2 - - - -
652B PHE* 2.8 33.4 + - + +
667B CYS* 4.0 15.9 - - - -
671B LEU* 4.7 7.2 - - + -
891B MET* 4.0 19.1 - - + -
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Residues in contact with VAL 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ARG 3.9 19.5 - - - +
368B GLY* 3.5 13.5 - - - +
369B SER* 4.0 6.7 - - - -
626B ALA* 3.2 37.7 - - + +
629B MET* 5.1 4.7 - - + -
645B HIS* 3.3 13.9 - - + +
646B GLN* 3.0 8.6 + - - +
648B ILE* 1.3 78.9 - - + +
650B ALA* 1.3 69.9 + - - +
651B ARG 2.6 1.2 + - - -
652B PHE* 5.2 0.2 - - - -
653B ALA* 3.0 37.4 + - + +
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Residues in contact with ALA 650 (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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366B ARG* 6.4 1.1 - - + -
646B GLN* 2.8 22.1 + - - +
647B VAL* 4.1 6.1 - - - +
649B VAL* 1.3 79.8 - - - +
651B ARG* 1.3 59.2 + - - +
653B ALA 4.5 6.3 - - - +
770B ARG* 6.1 0.2 - - - +
780B THR 4.3 19.5 - - - +
781B THR* 4.7 10.1 - - - +
782B GLY* 5.0 4.6 - - - +
892B TYR* 4.4 16.6 - - + -
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Residues in contact with ARG 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B VAL 2.8 21.7 + - - +
648B ILE 2.9 1.1 + - - +
649B VAL 2.6 2.2 + - - -
650B ALA* 1.3 74.2 - - - +
652B PHE* 1.3 77.4 + - + +
653B ALA 3.3 6.3 + - - -
663B ASN* 5.1 1.4 + - - -
670B ARG* 2.2 60.5 - - - +
770B ARG* 4.5 23.5 - - + +
774B ALA* 5.6 1.1 - - + -
890B THR 2.7 15.4 + - - -
891B MET* 2.9 57.0 + - - +
892B TYR* 4.5 9.6 - - + -
893B SER* 2.6 45.3 + - - +
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Residues in contact with PHE 652 (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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629B MET* 6.4 2.5 - - + -
648B ILE* 2.8 23.4 + - + +
651B ARG* 1.3 108.4 - - + +
653B ALA* 1.3 62.8 + - + +
654B ASP 4.2 0.6 + - - -
659B ILE* 3.3 18.9 - - + +
663B ASN* 3.8 49.6 + - + +
666B ARG* 4.2 12.3 - - + -
667B CYS* 3.5 40.8 - - + -
670B ARG* 3.8 11.2 - - + -
891B MET* 3.2 29.6 - - + -
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Residues in contact with ALA 653 (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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626B ALA* 4.2 9.2 - - + -
629B MET* 6.2 0.4 - - + -
649B VAL* 3.0 40.2 + - + +
650B ALA* 4.5 5.7 - - - +
651B ARG 3.3 3.1 + - - +
652B PHE* 1.3 84.4 - - - +
654B ASP* 1.3 73.2 + - - +
657B LEU 5.1 1.3 - - - -
658B ILE 4.8 4.3 - - - +
659B ILE* 3.8 20.9 - - + +
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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