Contacts of the helix formed by residues 573 - 587 (chain A) in PDB entry 2Q5H
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 PHE 573 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A PRO* 4.3 4.7 - - + -
567A LEU* 4.1 2.2 - - + -
568A SER* 3.5 40.2 - - - +
570A ASN* 2.6 40.7 + - + +
572A GLU* 1.3 73.0 - - - +
574A MET* 1.3 64.7 + - - -
575A PRO* 3.5 0.9 - - - -
576A PHE* 3.2 8.5 + - - +
577A VAL* 3.2 27.3 + - + +
618A ILE* 3.3 42.8 - - + -
619A ASP* 4.0 1.1 - - - -
620A PHE* 3.8 47.8 - + - -
623A VAL* 3.9 22.7 - - + -
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Residues in contact with MET 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A PRO* 5.7 0.4 - - + -
568A SER 5.9 0.2 - - - +
569A GLN* 3.9 43.3 - - - +
571A GLN* 3.4 15.2 + - + +
573A PHE* 1.3 81.2 - - - +
575A PRO* 1.3 73.7 - - + +
577A VAL* 3.0 31.0 + - + +
578A LYS* 2.8 29.1 + - + +
593A VAL* 5.5 3.4 - - + -
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Residues in contact with PRO 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A GLN 3.4 11.7 - - - +
572A GLU* 3.9 18.6 - - - +
573A PHE 3.7 0.2 - - - -
574A MET* 1.3 92.1 - - + +
576A PHE* 1.3 62.4 + - + +
578A LYS* 3.8 7.2 - - + +
579A GLU* 3.0 33.5 + - - +
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Residues in contact with PHE 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A GLU* 3.6 23.3 - - - -
573A PHE 3.2 7.3 + - - +
574A MET 3.2 0.4 - - - -
575A PRO* 1.3 82.8 - - + +
577A VAL* 1.3 58.0 + - - +
579A GLU* 3.9 4.8 - - - +
580A LEU* 3.0 30.1 + - - +
618A ILE* 4.4 12.8 - - + -
622A THR* 4.0 5.4 - - + -
623A VAL* 3.6 40.2 - - + -
628A HIS* 3.5 50.0 - + + -
645A ILE* 4.3 28.2 - - + +
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Residues in contact with VAL 577 (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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564A VAL* 4.1 8.8 - - + +
566A PRO* 4.0 17.3 - - + -
573A PHE* 3.2 18.2 - - + +
574A MET* 3.0 27.7 + - + +
576A PHE* 1.3 73.5 - - - +
578A LYS* 1.3 56.5 + - - +
580A LEU* 3.2 3.3 + - - +
581A SER* 2.8 36.8 + - - -
593A VAL* 3.6 39.5 - - + -
618A ILE* 3.8 22.2 - - + -
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Residues in contact with LYS 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A MET* 2.8 21.4 + - - +
575A PRO* 3.8 7.0 - - + +
577A VAL* 1.3 72.6 - - - +
579A GLU* 1.3 53.9 + - - +
581A SER* 3.0 7.6 + - - -
582A GLU* 2.7 71.0 + - + +
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Residues in contact with GLU 579 (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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575A PRO 3.0 19.5 + - - +
576A PHE* 3.9 4.0 - - - +
578A LYS* 1.3 76.3 - - - +
580A LEU* 1.3 52.3 + - - +
582A GLU* 3.2 15.6 + - - +
583A ALA* 2.7 38.5 + - - +
586A ARG* 3.9 20.2 + - - -
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Residues in contact with LEU 580 (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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564A VAL* 3.8 27.8 - - + -
576A PHE 3.0 20.0 + - - +
577A VAL* 3.6 4.9 - - - +
579A GLU* 1.3 76.3 - - - +
581A SER* 1.3 58.4 + - - +
583A ALA* 3.5 4.6 - - - +
584A LEU* 2.8 47.3 + - + +
616A VAL* 3.8 30.1 - - + -
618A ILE* 4.3 8.3 - - + -
645A ILE* 4.1 21.1 - - + +
648A LEU* 4.8 6.7 - - + -
649A PRO* 3.9 28.3 - - + -
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Residues in contact with SER 581 (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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564A VAL* 5.4 2.0 - - - +
577A VAL* 2.8 21.9 + - - -
578A LYS* 3.4 6.3 - - - -
580A LEU* 1.3 70.6 - - - +
582A GLU* 1.3 62.0 + - - +
584A LEU* 3.2 1.6 + - - -
585A THR* 2.9 27.6 + - - -
591A HIS* 2.5 43.3 + - - -
593A VAL* 4.5 13.7 - - - +
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Residues in contact with GLU 582 (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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578A LYS* 2.7 60.3 + - + +
579A GLU* 3.6 18.3 - - - +
581A SER* 1.3 74.2 - - - +
583A ALA* 1.3 51.7 + - - +
585A THR* 3.2 10.2 + - - +
586A ARG* 2.8 52.5 + - - +
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Residues in contact with ALA 583 (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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579A GLU* 2.7 24.9 + - - +
580A LEU* 3.5 4.3 - - - +
582A GLU* 1.3 72.8 - - - +
584A LEU* 1.3 63.4 + - - +
586A ARG* 3.0 23.3 + - - +
587A HIS* 2.9 32.3 + - + -
649A PRO* 3.4 27.4 - - + -
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Residues in contact with LEU 584 (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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562A CYS* 4.7 9.9 - - - -
564A VAL* 4.1 17.9 - - + -
580A LEU* 2.8 34.5 + - + +
581A SER 3.6 4.0 - - - +
583A ALA* 1.3 72.5 - - - +
585A THR* 1.3 61.5 + - - +
587A HIS* 3.1 6.2 + - - +
588A GLY 3.0 4.9 + - - -
589A VAL* 2.8 61.8 + - + +
591A HIS* 3.8 30.5 - - + +
616A VAL* 6.0 1.3 - - + -
648A LEU 5.5 0.2 - - - -
649A PRO* 4.1 22.2 - - + -
652A VAL* 4.6 12.3 - - + -
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Residues in contact with THR 585 (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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581A SER* 2.9 11.2 + - - -
582A GLU* 3.3 12.8 - - - +
584A LEU* 1.3 76.3 - - - +
586A ARG* 1.3 60.0 + - - +
588A GLY* 2.8 21.3 + - - +
589A VAL 4.7 2.5 - - - +
591A HIS* 3.5 18.8 - - - -
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Residues in contact with ARG 586 (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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579A GLU* 3.9 19.0 + - - -
582A GLU* 2.8 26.3 + - - +
583A ALA* 3.3 33.5 - - - +
585A THR* 1.3 76.6 - - + +
587A HIS* 1.3 66.8 + - + +
588A GLY 3.4 0.6 + - - -
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Residues in contact with HIS 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ALA* 2.9 25.0 + - + +
584A LEU* 3.5 9.4 - - - +
585A THR 3.0 0.4 - - - -
586A ARG* 1.3 88.4 + - + +
588A GLY* 1.3 62.1 + - - +
589A VAL* 3.2 13.8 + - + +
649A PRO* 3.8 21.3 + - + +
650A SER* 3.5 33.0 + - - -
653A GLN* 2.6 50.1 + - - +
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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