Contacts of the helix formed by residues 625 - 634 (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 SER 625 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624B MET* 1.3 83.5 - - - +
626B ALA* 1.3 57.5 + - - +
627B TYR* 3.7 22.0 + - - +
628B GLU* 2.5 53.9 + - - +
629B MET 3.3 2.6 + - - -
657B LEU* 4.0 15.2 + - - +
658B ILE* 3.9 2.2 - - - +
659B ILE 4.8 2.0 - - - +
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Residues in contact with ALA 626 (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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368B GLY* 3.0 9.6 - - - +
624B MET* 5.3 0.2 - - - -
625B SER* 1.3 74.4 + - - +
627B TYR* 1.3 53.9 + - - +
628B GLU 2.6 12.1 + - - -
629B MET* 2.9 29.1 + - + +
630B ARG* 3.8 3.8 + - - +
649B VAL* 3.2 38.9 - - + +
653B ALA* 4.2 13.9 - - + -
657B LEU 3.7 9.9 + - - +
658B ILE* 5.1 0.8 - - - +
659B ILE* 5.2 3.4 - - + +
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Residues in contact with TYR 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ARG* 4.5 0.3 - - - +
368B GLY* 2.9 51.1 + - - -
369B SER* 3.7 4.9 - - - +
371B ALA 3.3 20.3 + - - -
372B GLY* 4.7 2.0 - - - -
380B THR* 4.2 22.9 - - + -
382B TRP* 3.6 19.9 - - - -
383B VAL* 4.2 24.3 - - + +
493B ASN* 2.4 51.3 + - - +
625B SER* 2.9 17.5 + - - +
626B ALA* 1.3 72.8 - - - +
628B GLU* 1.3 70.3 + - - +
630B ARG* 4.2 5.2 - - - +
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Residues in contact with GLU 628 (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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379B ALA 4.9 4.0 - - - +
380B THR* 6.1 0.3 - - - +
382B TRP* 4.3 1.7 - - - -
451B ARG* 4.0 12.4 + - - -
616B PHE* 3.1 40.9 - - + -
624B MET* 5.8 0.4 - - + -
625B SER* 2.5 37.6 + - - +
626B ALA 2.6 1.4 + - - -
627B TYR* 1.3 83.8 - - - +
629B MET* 1.3 53.5 + - - -
630B ARG 2.8 3.4 - - - -
631B MET* 2.5 58.4 + - + +
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Residues in contact with MET 629 (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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616B PHE* 4.0 1.5 - - - -
624B MET* 3.7 19.7 - - + -
625B SER 3.3 4.4 + - - -
626B ALA* 2.9 25.7 + - + +
628B GLU* 1.3 74.8 - - - +
630B ARG* 1.4 65.6 + - - +
631B MET 3.3 0.7 + - - -
632B ALA* 3.6 1.7 + - - +
633B ILE* 3.0 69.1 + - + +
645B HIS* 6.5 0.2 - - + -
648B ILE* 4.0 17.0 - - + -
649B VAL* 5.1 3.8 - - + +
652B PHE* 6.4 2.5 - - + -
659B ILE* 5.1 10.3 - - + -
664B PHE* 3.6 43.3 - - + +
667B CYS* 5.1 6.3 - - + -
668B LEU* 5.0 2.0 - - + -
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Residues in contact with ARG 630 (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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369B SER 5.5 6.5 - - - +
382B TRP* 3.4 36.8 - - + -
383B VAL* 5.4 6.5 + - + -
448B HIS* 3.9 29.2 + - - +
450B LYS* 4.6 8.0 - - - +
514B ASP* 3.9 9.2 + - - -
515B ASP* 2.7 31.3 + - - -
626B ALA 3.8 2.7 + - - +
627B TYR 4.2 6.5 - - - +
628B GLU 4.0 5.6 - - - -
629B MET* 1.4 83.3 - - - +
631B MET* 1.4 56.1 - - - +
632B ALA 3.5 3.6 + - - -
633B ILE* 3.9 7.4 + - - +
634B GLU* 4.1 12.2 + - - +
640B LEU 3.6 9.1 + - - +
642B CYS* 4.1 7.9 - - - +
645B HIS* 2.9 75.0 + - + +
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Residues in contact with MET 631 (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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382B TRP* 3.1 47.6 - - + +
450B LYS* 4.8 10.3 - - + -
451B ARG* 4.2 16.4 - - - +
616B PHE* 2.7 35.7 - - + -
628B GLU* 2.5 71.7 + - + +
630B ARG* 1.4 63.7 - - - +
632B ALA* 1.4 55.6 + - - +
634B GLU* 3.6 21.8 - - + +
635B ALA 5.1 0.2 - - - -
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Residues in contact with ALA 632 (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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612B ILE* 4.7 6.4 - - + +
616B PHE* 3.8 22.7 - - + -
629B MET 3.7 8.5 - - - +
630B ARG 3.5 1.0 + - - -
631B MET* 1.4 79.2 - - - +
633B ILE* 1.3 61.4 + - - +
634B GLU 3.2 4.7 - - - +
635B ALA* 3.0 20.0 - - + +
636B ALA* 2.7 29.3 + - - +
664B PHE* 4.4 25.7 - - + -
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Residues in contact with ILE 633 (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* 3.0 55.6 - - + +
630B ARG 4.0 3.6 - - - +
632B ALA* 1.3 77.9 - - - +
634B GLU* 1.4 51.5 + - - +
636B ALA* 2.9 5.5 + - - +
637B GLY 2.9 9.0 + - - -
638B PHE* 2.9 52.6 + - + +
640B LEU* 4.0 16.4 - - + -
645B HIS* 4.2 12.6 - - + +
648B ILE* 3.3 33.4 - - + -
664B PHE* 5.1 0.2 - - - -
667B CYS* 5.2 0.4 - - - -
668B LEU* 3.8 23.6 - - + -
671B LEU* 4.0 2.9 - - + -
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Residues in contact with GLU 634 (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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450B LYS* 3.1 32.3 + - - -
515B ASP* 2.9 30.7 - - - +
630B ARG* 4.1 14.9 + - - +
631B MET* 3.6 18.7 - - - +
632B ALA 3.9 6.0 - - - +
633B ILE* 1.4 71.8 - - - +
635B ALA* 1.4 64.1 - - - +
636B ALA 3.3 0.2 - - - -
637B GLY* 3.4 12.6 + - - -
638B PHE 3.0 16.4 + - - +
639B LYS* 4.8 9.4 - - + -
640B LEU 5.9 0.4 - - - +
645B HIS* 5.9 2.0 - - + -
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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