Contacts of the helix formed by residues 397 - 403 (chain D) in PDB entry 3HB0
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 ASN 397 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D THR 4.5 12.2 + - - +
394D TYR* 3.0 25.2 + - + +
396D ASN* 1.3 82.9 - - - +
398D VAL* 1.3 61.3 + - - +
399D GLY* 3.0 4.4 + - - +
400D GLY* 2.8 36.5 + - - -
401D LEU 3.4 5.2 + - - -
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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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315D LEU* 5.1 3.6 - - + -
394D TYR* 3.2 13.0 + - - +
395D LYS 4.3 9.9 - - - +
396D ASN 4.0 0.4 - - - -
397D ASN* 1.3 75.3 - - - +
399D GLY* 1.3 62.0 + - - +
401D LEU* 3.0 19.2 + - + +
402D ILE* 3.1 27.1 + - + +
410D TRP* 3.7 24.8 - - + -
459D LEU* 3.5 33.7 - - + +
460D LEU* 3.9 27.4 - - + -
462D GLY* 5.9 0.9 - - - -
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Residues in contact with GLY 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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397D ASN* 3.0 2.9 + - - +
398D VAL* 1.3 80.6 - - - +
400D GLY* 1.3 59.9 + - - +
401D LEU 3.0 0.2 - - - -
402D ILE* 4.2 3.6 - - - -
403D GLY* 3.1 28.4 + - - +
404D THR* 5.1 0.3 - - - -
407D ARG* 3.7 38.4 - - - +
410D TRP* 4.6 3.4 - - - -
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Residues in contact with GLY 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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394D TYR* 3.7 15.6 + - - -
397D ASN* 2.8 34.1 + - - -
399D GLY* 1.3 75.6 - - - +
401D LEU* 1.3 59.2 + - - +
403D GLY* 4.5 2.1 + - - -
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Residues in contact with LEU 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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315D LEU* 4.5 26.0 - - + -
319D HIS* 3.2 55.9 + - + -
320D LEU* 5.7 1.6 - - + -
390D MET* 4.6 14.8 - - + +
394D TYR* 3.7 49.3 - - + -
397D ASN 3.4 1.6 + - - -
398D VAL* 3.0 12.0 + - + +
399D GLY 3.0 0.4 - - - -
400D GLY* 1.3 79.5 - - - +
402D ILE* 1.3 67.9 + - + +
403D GLY 3.3 0.8 + - - -
459D LEU* 4.6 14.6 - - + -
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Residues in contact with ILE 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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311D MET* 4.6 5.2 - - + -
315D LEU* 4.0 34.5 - - + -
319D HIS* 4.6 10.9 - - + -
398D VAL* 3.4 29.2 - - + +
399D GLY* 4.2 3.1 - - - -
401D LEU* 1.3 80.0 - - + +
403D GLY* 1.3 66.5 + - - +
405D PRO* 5.7 0.2 - - - +
406D LYS* 3.3 56.4 - - + +
407D ARG* 4.1 3.6 - - - -
410D TRP* 4.1 18.4 - - + -
460D LEU* 4.6 5.2 - - + -
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Residues in contact with GLY 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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399D GLY 3.1 15.4 + - - +
400D GLY 4.5 1.9 - - - -
401D LEU 3.3 3.2 + - - -
402D ILE* 1.3 80.2 - - - +
404D THR* 1.3 60.3 + - - -
405D PRO* 3.6 5.8 - - - -
406D LYS 3.6 0.8 + - - -
407D ARG* 2.9 29.5 + - - +
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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