Contacts of the helix formed by residues 641 - 652 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A ASP* 3.5 9.9 - - + +
515A ASP 4.0 20.8 - - - +
517A ILE* 3.2 21.8 - - + +
639A LYS 4.1 1.3 - - - +
640A LEU* 1.3 85.6 - - + +
642A CYS* 1.3 70.1 + - - +
643A GLN* 2.9 8.4 + - + +
644A LEU* 3.0 18.9 + - + +
645A HIS* 3.0 12.1 + - - -
884A GLN* 3.4 35.7 - - - +
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Residues in contact with CYS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A THR* 4.0 19.9 - - + +
383A VAL 4.9 0.2 - - - -
384A ASN 4.8 0.9 - - - -
385A PRO* 4.4 18.8 - - + -
448A HIS* 3.6 11.4 - - - -
512A GLU* 5.1 7.0 - - - +
513A LEU 5.5 0.2 - - - -
514A ASP* 2.2 43.9 + - - +
630A ARG* 3.2 30.7 - - - +
641A PRO* 1.3 68.7 - - - +
643A GLN* 1.3 62.7 + - - +
645A HIS* 3.4 10.6 - - - +
646A GLN* 2.9 29.1 + - + +
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Residues in contact with GLN 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 5.2 2.8 - - - +
364A THR* 5.3 1.6 + - - -
641A PRO* 2.9 8.5 + - + +
642A CYS* 1.3 77.9 - - - +
644A LEU* 1.3 63.7 - - + +
645A HIS 3.0 0.2 - - - -
646A GLN* 3.2 40.2 + - - +
647A VAL* 3.2 13.2 + - - +
780A THR* 4.0 18.2 + - - +
884A GLN* 5.3 5.4 - - - +
888A GLN* 3.4 33.6 + - - +
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Residues in contact with LEU 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A ILE* 3.6 30.1 - - + -
640A LEU* 3.8 22.0 - - + -
641A PRO* 3.0 19.8 + - + +
643A GLN* 1.3 79.5 - - + +
645A HIS* 1.3 60.6 - - - +
646A GLN 3.0 4.0 - - - -
647A VAL* 3.3 10.2 + - + +
648A ILE* 3.0 32.5 + - - +
884A GLN* 4.8 6.7 - - + +
887A LEU* 3.8 27.1 - - + -
888A GLN* 3.5 39.5 - - + +
891A MET* 5.8 2.7 - - + -
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Residues in contact with HIS 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A SER* 3.8 10.7 - - - +
370A THR* 6.2 0.9 - - + -
515A ASP* 5.8 0.4 - - - +
630A ARG* 3.3 69.1 + - + +
633A ILE* 4.4 15.7 - - + +
634A GLU* 6.3 0.2 - - + -
638A PHE 5.9 0.9 - - - -
639A LYS* 6.0 0.4 - - - +
640A LEU* 2.3 43.5 + - + +
641A PRO 3.0 23.5 + - - -
642A CYS* 2.9 13.2 + - - +
644A LEU* 1.3 77.0 - - - +
646A GLN* 1.2 71.9 + - - +
647A VAL 3.4 0.2 + - - -
648A ILE* 3.5 5.9 + - + +
649A VAL* 3.1 32.9 + - + +
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Residues in contact with GLN 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A THR* 3.1 32.9 + - - -
366A ARG* 3.1 31.5 + - + +
369A SER* 3.6 17.0 + - - +
370A THR* 3.1 33.6 + - + +
642A CYS* 2.9 20.2 + - - +
643A GLN* 3.2 28.9 + - - +
645A HIS* 1.2 88.1 - - - +
647A VAL* 1.4 53.3 + - - -
650A ALA* 3.4 25.5 + - - +
780A THR* 3.9 15.1 - - + +
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Residues in contact with VAL 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 5.2 2.7 - - + -
643A GLN* 3.2 30.1 - - - +
644A LEU* 3.3 19.0 + - + +
645A HIS 3.3 0.2 - - - -
646A GLN* 1.4 72.2 - - - +
648A ILE* 1.3 74.5 + - + +
649A VAL 3.3 1.8 - - - -
650A ALA 3.8 0.7 - - - -
651A ARG* 3.1 24.1 + - + +
780A THR* 4.5 9.9 - - + +
887A LEU 5.2 0.2 - - - +
888A GLN* 4.7 9.2 - - + +
891A MET* 3.3 36.3 - - + -
892A TYR* 3.7 32.4 - - + +
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Residues in contact with ILE 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A MET* 4.0 15.3 - - + -
633A ILE* 3.0 30.1 - - + -
640A LEU* 4.0 19.7 - - + -
644A LEU 3.0 20.2 - - - +
645A HIS* 3.8 9.2 - - + +
647A VAL* 1.3 89.2 - - + +
649A VAL* 1.2 66.3 + - + +
652A PHE* 3.1 37.1 + - + +
659A ILE* 5.9 0.9 - - + -
667A CYS* 3.6 28.9 - - - -
891A MET* 4.5 10.5 - - + -
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Residues in contact with VAL 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ARG 3.9 11.4 - - - +
368A GLY* 3.7 33.4 - - - +
369A SER* 3.9 11.0 - - - +
626A ALA* 3.7 17.0 - - + +
629A MET* 4.9 9.2 - - + -
645A HIS* 3.1 21.3 + - + +
646A GLN 4.3 0.2 - - - +
648A ILE* 1.2 82.3 - - + +
650A ALA* 1.3 68.0 + - - +
652A PHE* 5.2 0.2 - - - -
653A ALA* 3.1 37.1 + - + +
657A LEU* 5.9 0.9 - - - -
659A ILE* 5.3 2.2 - - + -
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Residues in contact with ALA 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A GLN 3.4 17.1 + - - +
647A VAL 3.5 0.2 + - - -
648A ILE 3.3 0.6 - - - -
649A VAL* 1.3 85.8 - - - +
651A ARG* 1.3 59.7 + - - +
653A ALA 5.0 2.9 - - - +
780A THR* 4.4 9.6 - - + +
781A THR 4.4 3.1 - - - -
782A GLY* 3.9 33.2 - - - +
892A TYR* 3.6 23.5 + - + +
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Residues in contact with ARG 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A VAL* 3.1 18.1 + - + +
648A ILE 3.9 0.9 - - - +
650A ALA* 1.3 81.3 - - - +
652A PHE* 1.3 89.5 + - + +
653A ALA 4.6 1.8 - - - +
663A ASN* 4.7 6.7 + - - +
666A ARG* 3.9 16.6 - - - +
670A ARG* 4.7 0.9 - - - +
767A ASP* 3.7 27.9 + - - +
770A ARG* 3.3 38.0 - - - +
771A SER* 4.1 11.9 - - - +
774A ALA* 4.8 3.8 - - - -
891A MET 4.8 1.3 - - - +
892A TYR* 4.1 14.6 - - + -
893A SER* 3.1 34.6 + - - +
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Residues in contact with PHE 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A MET* 5.6 0.9 - - + -
648A ILE* 3.1 28.9 + - + +
651A ARG* 1.3 94.6 - - + +
653A ALA* 1.3 70.4 + - - +
654A ASP* 3.6 0.9 + - - +
658A ILE 4.7 0.2 - - - +
659A ILE* 4.4 11.3 - - + +
663A ASN* 3.0 51.9 - - + +
666A ARG* 4.0 24.2 - - + -
667A CYS* 2.4 50.0 - - + -
670A ARG* 3.9 17.7 - - - -
891A MET* 3.4 25.6 - - + -
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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
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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