Contacts of the strand formed by residues 399 - 401 (chain D) in PDB entry 1IR1
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 VAL 399 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LEU* 3.4 24.5 - - + +
171D GLY 4.3 6.3 - - - +
199D PHE* 4.4 3.1 - - + -
239D TYR* 3.8 20.0 - - - +
325D HIS* 4.3 11.0 - - + +
375D LEU* 3.9 24.5 - - + -
376D PRO 3.0 4.7 + - - +
377D VAL* 3.4 21.4 - - + +
378D ALA 2.8 27.5 + - - +
398D SER* 1.3 80.3 - - - +
400D LEU* 1.3 64.7 + - - +
401D GLN* 4.0 16.4 - - + +
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Residues in contact with LEU 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D PRO* 3.8 24.5 - - + -
169D LEU 2.9 9.2 + - - +
170D LEU* 3.4 12.7 - - + +
171D GLY 2.8 21.5 + - - +
378D ALA* 3.5 20.0 - - + +
382D ILE* 5.0 0.9 - - + -
387D MET* 4.2 11.0 - - - -
390D LEU* 4.3 29.4 - - + +
391D THR* 4.7 4.0 - - - +
394D PHE* 4.7 5.2 - - + -
398D SER* 3.6 18.2 - - - +
399D VAL* 1.3 81.1 - - - +
401D GLN* 1.3 60.1 + - - +
402D PHE* 3.7 17.7 - - + -
424D LEU* 4.0 19.3 - - + -
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Residues in contact with GLN 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D GLY* 3.3 20.5 - - - -
172D CYS* 4.1 4.3 - - - +
173D THR* 4.5 2.1 + - - +
201D KCX 3.4 20.1 - - - +
239D TYR* 2.9 44.3 + - - -
292D HIS* 3.9 0.8 - - - -
327D HIS* 3.7 6.4 - - - -
377D VAL* 3.4 30.9 - - + +
378D ALA 2.9 8.5 + - - -
379D SER* 3.6 29.3 + - - +
380D GLY 4.3 1.6 + - - -
382D ILE* 3.3 22.7 - - - +
399D VAL* 4.0 4.3 - - + +
400D LEU* 1.3 76.2 - - - +
402D PHE* 1.3 63.7 + - - +
403D GLY 4.1 1.8 + - - -
501D CAP 4.4 0.6 + - - +
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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
------------------------------------------------------------
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