Contacts of the helix formed by residues 395 - 408 (chain D) in PDB entry 2G4C
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 395 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387D VAL* 3.2 23.4 - - + +
388D GLY 3.8 12.6 - - - +
390D GLY* 4.4 1.1 - - - -
391D PRO* 3.0 39.0 - - + +
392D THR 2.7 1.4 + - - -
394D GLU* 1.3 78.2 - - - +
396D ARG* 1.3 59.4 + - - +
398D VAL* 2.8 26.0 - - + +
399D CYS* 3.6 3.1 - - - -
443D VAL* 3.2 30.7 - - + +
444D THR* 3.2 38.1 - - - +
445D GLU* 4.0 3.6 - - - +
448D LEU* 4.3 14.4 - - + -
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Residues in contact with ARG 396 (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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387D VAL* 3.9 20.0 - - + -
392D THR* 2.7 38.5 + - + +
393D LEU* 3.2 29.3 - - - +
395D LEU* 1.3 76.8 - - - +
397D GLN* 1.3 57.4 + - - +
398D VAL 3.0 1.8 - - - -
399D CYS* 2.7 34.4 + - - +
400D GLN* 3.3 17.0 + - - +
417D TYR* 3.4 32.1 + - + +
418D LEU* 4.8 19.5 - - - +
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Residues in contact with GLN 397 (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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245C PRO* 4.1 23.3 + - + +
246C ARG* 3.8 26.1 + - - +
249C ASN* 5.0 4.9 + - - +
393D LEU 2.8 22.8 + - - +
394D GLU* 3.4 32.2 + - - +
396D ARG* 1.3 79.3 - - - +
398D VAL* 1.3 63.5 + - + +
400D GLN* 3.6 30.1 + - - +
401D GLY* 3.6 3.8 + - - -
448D LEU* 6.0 0.2 - - - +
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Residues in contact with VAL 398 (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 GLU 4.5 3.4 - - - +
395D LEU* 2.8 40.6 - - + +
397D GLN* 1.3 77.8 - - + +
399D CYS* 1.3 63.5 + - - +
401D GLY* 2.7 27.8 + - - +
402D LEU* 3.4 4.0 + - - +
443D VAL* 3.3 20.2 - - + -
447D THR* 6.0 0.4 - - + -
448D LEU* 5.8 4.7 - - + -
468D ILE* 3.6 30.5 - - + -
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Residues in contact with CYS 399 (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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385D LEU* 3.9 16.3 - - + +
386D ASP 4.4 4.5 - - - -
387D VAL* 3.7 9.6 - - - -
395D LEU 3.6 17.5 - - - -
396D ARG 2.7 13.3 + - - +
398D VAL* 1.3 76.4 - - - +
400D GLN* 1.3 50.3 + - - +
402D LEU* 2.7 30.5 + - - +
403D PHE* 2.7 16.0 + - - +
417D TYR* 3.3 44.0 - - + -
443D VAL* 4.2 18.4 - - - -
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Residues in contact with GLN 400 (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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245C PRO* 6.3 1.0 - - - +
396D ARG* 3.3 16.2 + - - +
397D GLN* 3.6 21.8 + - - +
398D VAL 3.2 0.2 - - - -
399D CYS* 1.3 77.9 - - - +
401D GLY* 1.3 57.2 + - - +
402D LEU 3.2 0.2 - - - -
403D PHE* 3.6 12.1 - - + -
404D ASN* 2.9 44.6 + - - +
417D TYR* 3.1 37.3 + - + +
418D LEU* 5.5 1.4 - - - +
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Residues in contact with GLY 401 (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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397D GLN 3.6 3.7 + - - -
398D VAL* 2.7 21.9 + - - -
400D GLN* 1.3 74.8 - - - +
402D LEU* 1.3 56.8 + - - -
404D ASN* 4.2 4.1 - - - +
405D GLU* 3.0 28.2 + - - +
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Residues in contact with LEU 402 (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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385D LEU* 4.4 9.9 - - + -
398D VAL* 3.4 4.0 + - + +
399D CYS* 2.7 11.0 + - - +
401D GLY* 1.3 72.3 - - - -
403D PHE* 1.3 59.9 + - - +
404D ASN 3.2 0.2 - - - -
405D GLU* 3.2 25.6 - - - +
406D LEU* 2.5 53.2 + - + +
441D VAL* 4.7 0.9 - - + -
443D VAL* 4.2 17.7 - - + -
453D ILE* 5.0 0.7 - - + -
468D ILE* 3.5 50.3 - - + +
471D LEU* 4.1 25.8 - - + -
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Residues in contact with PHE 403 (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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121B PHE 4.5 5.8 - - - -
122B ARG* 5.4 2.2 - - - -
123B GLU* 4.2 24.5 - - + -
385D LEU* 5.1 1.9 - - + +
399D CYS 2.7 8.1 + - - +
400D GLN* 3.5 20.0 - - + +
402D LEU* 1.3 76.1 - - - +
404D ASN* 1.3 67.9 + - - +
406D LEU* 3.4 6.8 - - - +
407D LEU* 2.7 61.9 + - + +
413D VAL* 3.5 43.9 - - + +
415D PRO* 4.1 20.4 - - + -
417D TYR* 3.8 25.4 - + + -
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Residues in contact with ASN 404 (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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121B PHE 5.4 1.2 - - - +
331C VAL* 6.0 4.2 - - - +
400D GLN* 2.9 29.5 + - - +
401D GLY* 4.2 4.8 - - - +
403D PHE* 1.3 88.8 - - - +
405D GLU* 1.3 58.0 + - - +
407D LEU* 4.2 9.4 - - - +
408D GLU* 2.7 54.7 + - + +
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Residues in contact with GLU 405 (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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401D GLY 3.0 22.1 + - - +
402D LEU* 3.2 28.9 + - - +
404D ASN* 1.3 76.3 - - - +
406D LEU* 1.3 59.8 + - + +
408D GLU* 3.6 8.5 + - - +
409D ASN* 2.5 40.3 + - - +
468D ILE 4.5 4.4 - - - +
469D SER* 5.3 5.6 + - - -
472D LYS* 3.9 27.4 + - + +
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Residues in contact with LEU 406 (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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383D VAL* 4.4 5.8 - - + -
385D LEU* 4.0 18.2 - - + -
402D LEU* 2.5 38.2 + - + +
403D PHE 3.4 2.7 - - - +
405D GLU* 1.3 77.1 - - + +
407D LEU* 1.3 56.4 + - - +
409D ASN* 2.7 31.2 + - - +
410D GLY 3.3 4.3 + - - -
411D ILE* 3.3 27.6 + - + +
413D VAL* 3.5 28.3 - - + -
471D LEU* 4.8 5.6 - - + -
472D LYS* 3.6 35.9 - - + +
475D LEU* 4.3 7.9 - - + -
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Residues in contact with LEU 407 (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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120B VAL* 4.0 29.3 - - + +
121B PHE* 3.3 26.5 - - - +
123B GLU* 4.3 16.6 - - + +
403D PHE* 2.7 55.5 + - + +
404D ASN* 3.7 8.1 - - - +
406D LEU* 1.3 72.1 - - - +
408D GLU* 1.3 57.1 + - + +
409D ASN 2.7 10.7 + - - -
410D GLY* 2.9 13.8 + - - +
411D ILE 4.0 17.5 - - - +
412D SER* 5.1 1.6 - - - -
413D VAL* 4.6 6.3 - - + +
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Residues in contact with GLU 408 (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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323C HIS* 4.4 19.5 + - - -
330C ASN* 5.1 14.0 + - - +
404D ASN* 2.7 43.8 + - + +
405D GLU* 3.9 8.0 - - - +
407D LEU* 1.3 71.1 - - + +
409D ASN* 1.3 63.3 + - - +
410D GLY 3.7 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