Contacts of the strand formed by residues 397 - 401 (chain D) in PDB entry 2R2N
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 TYR 397 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357D TRP* 3.2 50.5 - + + -
358D ILE 3.2 7.4 - - - -
359D LYS* 3.3 43.3 + - + +
366D VAL* 3.1 11.3 - - - +
384D GLY 2.9 23.1 + - - -
388D TYR* 3.9 21.3 - + - -
395D SER* 3.3 7.8 - - - +
396D PRO* 1.3 103.3 - - + +
398D LEU* 1.3 60.9 + - - +
428D GOL 3.3 27.6 + - - -
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Residues in contact with LEU 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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356D LEU 3.6 1.2 - - - +
357D TRP* 3.5 8.3 - - - -
358D ILE* 2.9 38.6 + - + +
360D VAL* 4.0 19.1 - - + -
366D VAL* 3.6 22.2 - - + -
370D ILE* 3.2 41.3 - - + -
381D MET* 2.9 37.2 - - + -
382D LEU 3.3 13.2 - - - +
397D TYR* 1.3 74.7 - - - +
399D ARG* 1.3 59.1 + - - +
400D ALA 4.0 0.2 - - - -
417D LEU* 3.9 16.8 - - + -
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Residues in contact with ARG 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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19C ILE* 4.4 0.2 - - - +
36C LEU 3.7 4.6 - - - +
37C ALA 3.2 25.1 + - - -
38C GLY* 3.6 15.4 + - - -
39C GLY 3.8 0.4 - - - +
427C KYN 3.0 35.0 + - - -
202D ASN* 2.9 23.7 + - - +
203D PRO* 3.5 27.6 - - + +
355D PHE* 3.5 35.4 - - + -
356D LEU 3.5 2.7 - - - +
357D TRP* 4.1 12.2 - - + -
381D MET* 3.7 2.3 - - - +
382D LEU* 2.6 54.2 + - + +
387D PHE* 3.4 16.9 - - + -
398D LEU* 1.3 73.5 - - - +
400D ALA* 1.3 61.7 + - - +
401D SER 5.5 1.0 - - - +
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Residues in contact with ALA 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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36C LEU* 3.4 11.2 - - + -
333D ILE* 4.0 18.9 - - + +
355D PHE* 3.6 3.3 - - - -
356D LEU* 2.7 44.8 + - + +
358D ILE* 4.1 13.0 - - + -
381D MET* 3.9 25.1 - - - -
398D LEU 4.0 0.4 + - - -
399D ARG* 1.3 75.0 - - - +
401D SER* 1.3 62.0 + - - +
402D PHE 3.7 0.3 + - - -
414D PHE* 4.5 0.9 - - + -
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Residues in contact with SER 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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36C LEU* 2.8 40.1 + - - +
38C GLY 3.4 26.0 + - - -
40C LEU 4.6 1.6 + - - -
333D ILE* 4.1 4.8 - - - +
354D MET* 3.5 8.9 + - - +
355D PHE* 3.8 14.1 - - - -
399D ARG* 4.3 0.8 - - - +
400D ALA* 1.3 73.4 - - - +
402D PHE* 1.3 58.4 + - - +
403D SER* 3.0 31.4 + - - -
404D SER 4.7 0.9 + - - -
405D ALA* 5.2 1.7 + - - +
410D MET* 5.2 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