Contacts of the helix formed by residues 475 - 483 (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 ASP 475 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ARG* 4.4 9.3 + - - +
422D MET* 3.8 22.0 - - + +
425D SER* 3.8 14.3 + - - +
426D ARG* 2.8 51.7 + - - +
432D GLY* 5.2 2.2 - - - -
468D TYR* 2.6 28.9 + - - +
473D ASN 3.2 4.6 + - - +
474D ILE* 1.3 73.9 - - - +
476D ILE* 1.3 60.4 + - - +
477D TRP 3.4 1.1 - - - +
478D MET 3.2 3.6 + - - +
479D GLY 2.9 25.5 + - - -
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Residues in contact with ILE 476 (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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327D VAL* 4.1 13.2 - - + -
330D ASN* 3.5 20.2 - - + +
331D ALA* 4.9 8.3 - - + -
425D SER* 4.0 13.8 + - - -
430D LEU* 4.1 18.6 - - + -
431D PRO 4.4 5.2 + - - +
433D TYR* 5.0 4.7 - - - +
436D TRP* 3.7 46.0 - - + -
474D ILE 3.5 3.6 + - - -
475D ASP* 1.3 72.0 - - - +
477D TRP* 1.3 60.3 + - - +
479D GLY* 5.2 0.7 - - - -
480D GLY* 2.8 28.3 + - - -
494D LEU* 3.8 19.1 - - + -
495D LEU* 4.8 2.4 - - + +
498D ILE* 3.9 11.9 - - + -
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Residues in contact with TRP 477 (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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69B VAL* 4.1 4.3 - - + -
330D ASN* 3.3 40.3 + - - +
331D ALA* 4.9 3.6 - - - +
333D ARG* 2.9 32.8 + - + -
334D TYR 4.1 0.9 - - - -
336D HIS* 4.4 10.1 - - + -
337D THR* 4.1 12.3 - - + -
397D ILE* 3.8 21.1 - - + -
398D ALA* 4.8 1.3 - - + -
418D PRO* 3.8 40.4 - - + -
421D ASN* 3.5 27.3 + - + -
422D MET* 4.5 5.6 - - + -
425D SER* 5.2 0.2 + - - -
475D ASP* 3.4 1.0 - - - +
476D ILE* 1.3 80.7 - - - +
478D MET* 1.3 85.6 + - + +
480D GLY* 5.1 0.4 - - - -
481D VAL* 3.0 56.8 + - + +
495D LEU* 5.7 1.6 - - + -
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Residues in contact with MET 478 (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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64B VAL* 3.8 20.9 - - + -
68B ILE* 3.8 9.9 - - + -
69B VAL* 3.8 22.2 - - + -
397D ILE* 3.8 26.5 - - + -
422D MET* 3.8 15.5 - - + +
464D LEU* 4.0 17.3 - - + -
468D TYR* 3.6 22.7 - - - +
474D ILE* 4.4 0.9 - - + -
475D ASP 3.2 8.5 + - - +
477D TRP* 1.3 86.0 - - + +
479D GLY* 1.3 56.8 + - - +
481D VAL* 3.8 10.5 - - + -
482D SER* 2.6 43.8 + - - +
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Residues in contact with GLY 479 (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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433D TYR* 3.8 21.9 - - - -
455D LEU* 5.1 0.3 - - - +
464D LEU* 5.8 0.7 - - - -
474D ILE* 3.4 21.6 - - - +
475D ASP 2.9 12.0 + - - -
478D MET* 1.3 75.4 - - - +
480D GLY* 1.3 64.6 + - - +
482D SER* 3.2 18.8 + - - -
483D GLU* 3.4 13.7 + - - +
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Residues in contact with GLY 480 (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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433D TYR* 4.5 1.6 - - - -
476D ILE 2.8 18.2 + - - -
477D TRP 3.8 0.2 - - - -
479D GLY* 1.3 76.9 - - - +
481D VAL* 1.3 61.4 + - - +
482D SER 3.1 1.0 + - - -
483D GLU* 3.3 18.9 + - - +
492D GLY 4.7 3.5 + - - -
494D LEU* 4.6 12.5 - - - +
495D LEU* 3.4 33.4 - - - +
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Residues in contact with VAL 481 (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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334D TYR* 4.1 13.9 - - + -
337D THR* 3.9 19.7 - - + -
392D ASN* 3.1 25.3 + - - +
394D GLN* 5.6 3.5 - - - +
397D ILE* 4.0 10.9 - - + +
477D TRP* 3.0 59.5 + - + +
478D MET* 3.5 23.6 - - + +
480D GLY* 1.3 75.1 - - - +
482D SER* 1.3 61.7 + - - +
483D GLU 3.4 4.2 + - - +
495D LEU* 4.1 9.9 - - + -
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Residues in contact with SER 482 (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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394D GLN* 3.0 28.3 + - - +
397D ILE* 4.8 3.8 - - - +
455D LEU* 4.0 6.8 - - - +
460D LEU* 3.5 27.2 - - - +
464D LEU* 4.2 18.0 - - - +
478D MET* 2.6 37.3 + - - +
479D GLY* 3.3 11.0 - - - -
480D GLY 3.1 0.6 - - - -
481D VAL* 1.3 78.2 - - - +
483D GLU* 1.3 58.4 + - - +
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Residues in contact with GLU 483 (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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394D GLN* 4.1 1.8 - - - +
433D TYR* 2.7 35.3 + - - +
437D ARG* 2.8 24.2 + - - -
454D VAL* 5.1 2.5 - - + -
455D LEU* 4.0 8.1 - - + -
479D GLY 3.6 12.1 - - - +
480D GLY 3.3 9.3 + - - +
481D VAL 4.0 5.4 - - - +
482D SER* 1.3 79.8 - - - +
484D PRO* 1.3 72.9 - - + +
485D LEU* 3.5 14.4 + - - +
492D GLY* 3.6 11.5 + - - -
493D PRO* 3.1 13.6 - - + +
494D LEU* 2.8 35.3 + - - +
495D LEU 4.5 0.5 + - - -
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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