Contacts of the helix formed by residues 521 - 529 (chain A) in PDB entry 2GQ3
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 LEU 521 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASP* 3.9 12.6 - - - +
516A TRP* 3.5 12.8 + - + -
518A MET* 3.1 28.5 + - + +
519A THR 3.4 0.4 - - - -
520A GLU* 1.3 86.0 - - + +
522A MET* 1.3 59.7 + - - +
523A ALA 3.4 2.2 - - - -
524A ASP* 3.5 28.4 + - + +
525A MET 3.2 17.5 + - - -
628A VAL* 4.0 31.6 - - + -
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Residues in contact with MET 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A THR* 3.9 20.0 - - + -
146A ASP* 3.0 12.8 + - - +
147A VAL* 3.8 7.2 - - + -
516A TRP* 3.7 19.5 - - + +
518A MET 3.6 17.0 - - - +
519A THR* 3.4 27.6 - - - +
520A GLU 4.4 3.1 - - - +
521A LEU* 1.3 71.8 - - - +
523A ALA* 1.3 67.7 + - - +
524A ASP 3.0 1.3 - - - -
525A MET* 3.5 12.0 - - - +
526A VAL* 2.9 29.8 + - - +
543A PRO* 5.2 0.7 - - + -
544A SER* 5.5 1.3 - - - +
546A THR* 4.8 2.5 - - + -
547A ALA* 3.9 28.0 - - + -
550A LEU* 3.7 29.4 - - + -
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Residues in contact with ALA 523 (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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146A ASP* 2.9 36.5 + - - +
147A VAL* 4.0 15.7 - - - +
521A LEU 3.4 0.2 - - - -
522A MET* 1.3 77.5 - - - +
524A ASP* 1.3 62.9 + - - +
526A VAL* 3.4 4.5 + - - +
527A GLU* 3.0 29.8 + - - +
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Residues in contact with ASP 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ASP* 5.5 1.3 - - - +
516A TRP* 3.7 15.3 - - + -
518A MET* 6.2 0.2 - - - -
521A LEU* 3.5 38.1 + - + +
522A MET 3.0 0.2 - - - -
523A ALA* 1.3 81.6 - - - +
525A MET* 1.3 59.2 + - - +
527A GLU* 3.2 14.1 + - - +
528A THR* 2.8 40.2 + - - +
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Residues in contact with MET 525 (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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516A TRP* 3.5 44.8 - - + +
521A LEU 3.2 10.8 + - - +
522A MET* 3.2 19.0 + - - +
524A ASP* 1.3 75.4 - - - +
526A VAL* 1.3 63.6 + - + +
529A LYS* 2.8 58.5 + - + +
542A VAL* 4.7 1.3 - - - -
547A ALA* 3.4 40.4 - - - +
550A LEU* 3.6 24.7 - - + -
551A HIS* 3.6 12.1 - - - +
554A HIS* 3.4 2.1 - - + -
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Residues in contact with VAL 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 3.9 20.6 - - + -
171A TYR* 3.8 21.8 - - - +
522A MET 2.9 19.9 + - - +
523A ALA* 3.8 5.8 - - - +
525A MET* 1.3 76.6 - - + +
527A GLU* 1.3 62.0 + - - +
530A ILE* 4.5 2.8 - - - +
550A LEU* 3.9 28.9 - - + +
553A LEU* 4.4 12.3 - - + -
554A HIS* 2.7 33.8 + - + +
557A GLN* 5.7 2.6 + - - +
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Residues in contact with GLU 527 (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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523A ALA 3.0 16.2 + - - +
524A ASP* 3.2 16.0 + - - +
526A VAL* 1.3 79.2 - - - +
528A THR* 1.3 59.8 + - - +
530A ILE* 3.6 17.5 - - - +
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Residues in contact with THR 528 (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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516A TRP* 4.0 19.9 - - + -
524A ASP* 2.8 23.7 + - - +
527A GLU* 1.3 77.1 + - - +
529A LYS* 1.3 60.1 + - - +
530A ILE* 2.9 12.5 + - - +
531A ALA* 3.1 21.3 + - + +
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Residues in contact with LYS 529 (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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514A GLY 2.8 15.2 + - - -
515A MET 4.4 0.2 - - - -
516A TRP* 4.0 21.0 - - + +
525A MET* 2.8 48.9 + - + +
528A THR* 1.3 71.4 - - - +
530A ILE* 1.3 63.8 + - - +
531A ALA* 3.1 1.1 - - - -
532A GLN* 2.7 47.7 + - - +
533A PRO* 3.4 9.0 - - - +
540A ALA* 3.5 2.6 - - - +
541A TRP 2.8 28.8 + - - -
542A VAL* 3.8 5.2 - - - -
551A HIS* 3.6 32.5 - - + +
554A HIS* 3.9 7.4 - - + -
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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