Contacts of the helix formed by residues 521 - 529 (chain D) in PDB entry 1D7W
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 521 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520D PHE* 1.3 76.6 - - - +
522D MET* 1.3 59.6 + - - +
523D GLN* 3.3 21.1 - - - +
524D GLN* 2.9 38.9 + - - +
525D ARG* 2.8 29.5 + - - +
574D SER* 4.7 1.4 + - - -
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Residues in contact with MET 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D SER* 1.3 73.5 - - - +
523D GLN* 1.3 79.9 + - - +
525D ARG* 3.5 21.3 + - - +
526D GLN* 3.3 20.3 + - - +
2604D ACT 3.5 36.9 - - + +
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Residues in contact with GLN 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D SER* 3.3 20.0 - - - +
522D MET* 1.3 105.1 + - - +
524D GLN* 1.3 61.6 + - - +
526D GLN* 3.4 10.7 + - - +
527D ALA* 3.3 18.2 + - - +
574D SER* 3.5 26.6 + - - +
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Residues in contact with GLN 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D GLU* 5.2 1.6 + - - -
282D LYS* 5.9 0.2 + - - -
519D VAL 4.8 0.9 - - - +
520D PHE* 3.5 18.9 - - + -
521D SER* 2.9 42.6 + - - +
523D GLN* 1.3 75.7 - - - +
525D ARG* 1.3 59.7 + - - +
527D ALA 3.4 0.7 + - - -
528D LEU* 3.1 33.8 + - - +
574D SER* 3.5 29.0 + - - +
575D TRP* 3.1 57.1 - - + +
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Residues in contact with ARG 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D TRP* 3.8 38.8 - - + +
515D GLU* 4.1 21.2 + - - +
516D ASN 4.6 9.3 + - - -
517D GLU* 4.9 9.6 - - - +
518D GLY 5.0 0.2 - - - +
520D PHE* 2.8 42.0 + - + +
521D SER 2.8 15.2 + - - +
522D MET* 3.5 29.5 - - - +
524D GLN* 1.3 74.2 - - - +
526D GLN* 1.3 59.5 + - - +
528D LEU* 3.4 3.2 + - - +
529D ALA* 3.0 31.8 + - - +
2604D ACT 3.5 29.3 + - - +
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Residues in contact with GLN 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D MET 3.3 12.6 + - - +
523D GLN* 3.6 13.5 - - - +
524D GLN 3.3 0.2 - - - -
525D ARG* 1.3 78.8 - - - +
527D ALA* 1.3 67.6 + - - +
529D ALA* 3.6 6.5 + - - +
530D GLN* 3.2 40.1 + - - +
571D ASN* 6.1 0.7 - - - +
2604D ACT 5.0 1.9 + - - +
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Residues in contact with ALA 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523D GLN 3.3 8.9 + - - +
524D GLN 3.7 7.6 - - - +
525D ARG 3.2 0.4 - - - -
526D GLN* 1.3 88.9 - - - +
528D LEU* 1.3 60.4 + - - +
530D GLN* 3.3 19.8 + - - +
531D ILE 4.1 0.5 + - - -
570D LEU* 3.1 18.8 - - + +
571D ASN* 3.3 33.4 + - + +
574D SER* 4.4 2.2 - - - +
575D TRP* 3.7 12.1 - - + -
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Residues in contact with LEU 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D ILE* 3.9 28.0 - - + +
286D ALA* 3.7 16.2 - - + -
287D MET* 5.2 1.3 - - + -
290D ILE* 3.4 16.2 - - + +
514D TRP* 4.3 8.7 - - + -
520D PHE* 3.6 45.8 - - + -
524D GLN 3.1 20.5 + - - +
525D ARG 3.8 4.5 - - - +
527D ALA* 1.3 72.5 - - - +
529D ALA* 1.3 56.3 + - - +
530D GLN 3.0 5.2 - - - -
531D ILE* 2.9 42.9 + - + +
570D LEU* 4.4 7.2 - - + -
575D TRP* 3.8 11.7 - - + -
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Residues in contact with ALA 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D ILE* 4.3 5.6 - - - +
294D ARG* 3.2 22.8 + - - +
514D TRP* 4.7 10.7 - - + -
525D ARG 3.0 17.9 + - - +
526D GLN* 3.8 9.2 - - - +
527D ALA 3.4 0.4 - - - -
528D LEU* 1.3 74.7 - - - +
530D GLN* 1.3 67.5 + - - +
531D ILE 3.3 0.7 - - - -
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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