Contacts of the helix formed by residues 532 - 541 (chain D) in PDB entry 1D2V
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 532 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291D ILE* 4.5 1.6 - - - -
294D ARG* 3.9 13.5 - - - +
295D ASP* 5.5 0.4 - - - -
530D GLN 4.0 2.4 + - - -
531D ILE* 1.3 82.0 - - - +
533D LEU* 1.3 64.8 + - - +
534D PRO* 3.2 14.6 - - - +
535D ARG* 2.9 29.9 + - - +
536D ILE* 3.0 28.6 + - - +
549D ASN* 3.7 19.7 + - - -
567D LEU* 5.4 2.3 - - - +
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Residues in contact with LEU 533 (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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85B MET* 3.8 36.6 - - + -
89B TRP* 4.0 21.5 - - + -
249D MET* 3.7 19.1 - - + -
252D LEU* 4.0 14.8 - - + -
253D LEU* 5.8 2.0 - - + -
291D ILE* 3.8 30.1 - - + +
294D ARG* 5.3 0.4 - - - +
295D ASP* 5.3 1.6 + - - +
532D SER* 1.3 72.3 - - - +
534D PRO* 1.4 69.8 - - + +
536D ILE* 3.1 8.7 + - + +
537D ILE* 3.0 29.5 + - + +
551D ILE* 3.8 17.5 - - + -
552D PHE* 4.1 10.8 - - + -
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Residues in contact with PRO 534 (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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532D SER* 3.2 13.0 - - - +
533D LEU* 1.4 95.5 - - + +
535D ARG* 1.3 61.6 + - - +
537D ILE* 3.2 15.2 + - + +
538D CYS* 2.9 29.8 + - - -
546D VAL* 3.9 14.7 - - + +
547D SER 3.6 21.8 - - - +
549D ASN* 3.3 21.8 - - - +
551D ILE* 3.8 24.9 - - + -
567D LEU* 4.5 5.4 - - + -
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Residues in contact with ARG 535 (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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530D GLN 5.2 3.6 - - - +
531D ILE* 5.5 1.8 - - - -
532D SER* 2.9 29.7 + - - +
534D PRO* 1.3 77.5 - - - +
536D ILE* 1.3 64.8 + - + +
538D CYS* 3.1 41.8 + - - +
539D ASP* 3.0 59.2 + - - +
564D CYS* 3.3 17.4 + - - +
567D LEU* 3.2 30.4 + - + +
568D PRO 3.5 23.6 - - - +
569D ALA* 3.4 19.8 - - - +
570D LEU* 4.8 3.6 - - + +
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Residues in contact with ILE 536 (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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252D LEU* 3.7 24.3 - - + +
253D LEU* 4.7 14.1 - - + -
256D GLU* 4.0 16.4 - - + -
287D MET* 3.8 40.6 - - + -
291D ILE* 4.1 22.9 - - + -
531D ILE* 4.9 1.3 - - + -
532D SER 3.0 21.9 + - - +
533D LEU* 3.1 8.9 + - + +
535D ARG* 1.3 72.2 - - + +
537D ILE* 1.3 67.3 + - - +
539D ASP* 3.1 8.9 + - - +
540D ASN* 2.9 39.5 + - - +
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Residues in contact with ILE 537 (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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85B MET* 4.5 9.0 - - + -
252D LEU* 3.8 25.1 - - + -
381D LEU* 4.4 10.1 - - + -
385D MET* 3.7 42.8 - - + -
533D LEU* 3.0 19.9 + - + +
534D PRO* 3.4 8.3 - - + +
536D ILE* 1.3 77.0 - - - +
538D CYS* 1.3 60.6 + - - +
539D ASP 3.2 0.2 + - - -
540D ASN 3.3 0.5 + - - -
541D THR* 2.7 51.4 + - + +
543D ILE* 4.5 4.7 - - + -
546D VAL* 4.2 9.2 - - + -
551D ILE* 3.9 16.4 - - + -
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Residues in contact with CYS 538 (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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534D PRO 2.9 18.4 + - - -
535D ARG* 3.2 32.0 + - - +
537D ILE* 1.3 78.7 - - - +
539D ASP* 1.3 59.4 - - - +
540D ASN 3.6 0.3 + - - -
541D THR 3.9 10.6 - - - +
543D ILE 4.1 5.8 - - - +
546D VAL* 3.4 16.8 - - - -
564D CYS* 2.1 55.0 - - + +
567D LEU* 4.2 2.9 - - - -
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Residues in contact with ASP 539 (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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256D GLU* 4.4 1.1 - - - +
259D ARG* 3.7 44.7 + - - +
535D ARG* 3.0 53.7 + - - +
536D ILE* 3.1 3.0 + - - +
538D CYS* 1.3 75.9 - - - +
540D ASN* 1.3 71.9 + - - +
541D THR 3.8 0.7 - - - -
569D ALA* 4.0 10.6 - - - +
570D LEU 5.1 0.7 + - - -
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Residues in contact with ASN 540 (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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208D ARG* 3.4 11.3 - - - +
252D LEU* 3.9 10.1 - - + +
255D ARG* 2.9 61.4 + - + +
256D GLU* 3.2 33.7 + - - +
259D ARG* 3.8 10.6 - - - +
536D ILE* 2.9 36.5 + - - +
539D ASP* 1.3 86.4 - - - +
541D THR* 1.3 61.2 + - - +
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Residues in contact with THR 541 (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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208D ARG* 3.6 20.4 + - - +
252D LEU* 4.2 8.5 - - + -
255D ARG* 4.3 5.6 - - - +
377D ILE* 4.4 0.2 - - + -
378D ASP* 3.2 16.8 - - - +
381D LEU* 3.7 30.3 - - + -
537D ILE* 2.7 26.5 + - + +
538D CYS 3.9 10.7 - - - +
539D ASP 5.2 0.2 - - - -
540D ASN* 1.3 85.1 - - - +
542D GLY* 1.3 61.4 + - - +
543D ILE* 3.3 25.1 + - - +
544D THR* 5.9 0.2 - - - +
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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