Contacts of the helix formed by residues 478 - 482 (chain D) in PDB entry 4L28
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 GLN 478 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292C GLU* 4.1 4.0 + - - +
295C GLN* 3.1 51.5 + - + +
427D PRO 4.2 3.2 + - - +
428D THR* 2.7 54.2 - - - +
429D ILE 3.7 4.5 - - - +
430D THR* 4.3 2.7 - - - +
431D CYS* 3.8 6.2 - - - -
476D SER 3.7 0.8 + - - +
477D ASP* 1.3 77.5 - - - +
479D VAL* 1.3 64.6 + - - +
480D GLY* 3.2 7.1 + - - +
481D LYS* 3.4 23.5 + - + +
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Residues in contact with VAL 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D VAL* 5.1 0.9 - - + -
426D LEU 4.9 0.7 - - - +
427D PRO* 3.8 9.8 + - + +
429D ILE* 3.1 28.1 + - + +
430D THR 4.0 5.8 - - - -
431D CYS* 4.1 6.1 - - - +
434D THR* 3.5 24.5 - - + +
448D VAL* 4.2 12.8 - - + -
459D VAL* 3.4 31.0 - - + -
464D MET* 3.5 17.3 - - + -
478D GLN* 1.3 69.9 - - - +
480D GLY* 1.3 64.7 + - - +
481D LYS 3.1 3.1 - - - -
482D VAL* 3.0 16.2 + - - +
483D ILE* 3.2 8.1 + - + -
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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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427D PRO* 3.8 14.9 + - - -
478D GLN* 3.2 5.3 - - - +
479D VAL* 1.3 78.6 - - - +
481D LYS* 1.3 60.6 + - - +
482D VAL 3.2 0.4 - - - -
483D ILE* 3.2 28.3 - - - +
485D LYS* 4.7 7.1 + - - -
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Residues in contact with LYS 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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194B ASN* 5.9 0.5 + - - -
472D LYS 4.3 7.6 - - - -
473D VAL* 4.0 21.7 - - + +
477D ASP* 3.9 36.8 - - + +
478D GLN* 3.4 14.8 + - + +
479D VAL 3.1 0.6 + - - -
480D GLY* 1.3 80.0 - - - +
482D VAL* 1.3 60.4 + - + +
483D ILE 3.7 0.2 - - - -
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Residues in contact with VAL 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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194B ASN* 4.6 5.3 - - - +
431D CYS* 4.4 11.7 - - - -
458D MET 4.7 0.3 - - - +
459D VAL* 4.6 6.1 - - + +
463D ASN* 3.5 25.6 + - - +
464D MET* 4.3 25.6 - - + -
467D SER* 3.8 24.7 - - - +
473D VAL* 3.8 24.0 - - + -
479D VAL* 3.3 16.6 - - + +
481D LYS* 1.3 83.4 - - + +
483D ILE* 1.3 65.3 + - - +
484D TYR* 3.6 4.5 + - - -
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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