Contacts of the strand formed by residues 202 - 207 (chain B) in PDB entry 4IVR
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 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 3.5 11.1 - - - +
51B ARG 2.8 25.4 + - - +
52B VAL* 3.8 1.7 - - - -
53B TYR* 2.9 32.9 + - - -
200B GLY 3.1 11.0 + - - -
201B THR* 1.3 72.1 - - - +
203B ILE* 1.3 61.5 + - - +
323B HIS* 3.4 13.2 - - - +
325B PHE* 3.7 17.0 - - + -
347B MET* 3.5 24.0 - - - +
348B VAL* 2.9 43.5 + - - +
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.6 8.7 - - + +
55B ASP* 4.1 15.7 - - + -
164B HIS* 3.8 20.9 - - + -
166B ILE* 4.1 10.3 - - + -
201B THR* 4.1 13.7 - - + +
202B ASN* 1.3 78.7 - - - +
204B VAL* 1.3 62.8 + - - +
205B LEU* 3.9 26.7 + - + -
242B LEU* 5.8 1.1 - - + -
322B MET* 3.5 42.0 - - + -
323B HIS 2.8 12.6 + - - +
324B VAL* 3.3 11.9 - - + +
325B PHE* 2.9 26.2 + - - +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 3.9 6.7 - - + -
53B TYR 2.8 12.5 + - - +
54B ILE* 3.8 26.0 - - + -
55B ASP* 2.8 35.0 + - - +
203B ILE* 1.3 73.7 - - - +
205B LEU* 1.3 63.5 + - - +
325B PHE* 3.2 11.4 - - + +
327B LEU* 3.6 38.1 - - + +
329B TYR* 4.9 3.4 - - - +
340B LEU* 4.0 7.2 - - + -
343B LEU* 4.6 3.6 - - + -
347B MET* 3.7 31.0 - - + -
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASP* 4.0 5.4 - - + -
56B GLY* 3.5 22.7 - - - +
57B PRO* 6.0 0.4 - - + -
203B ILE* 3.9 18.4 - - + -
204B VAL* 1.3 80.1 - - - +
206B GLY* 1.3 60.1 + - - +
239B TYR* 3.7 33.4 - - + +
242B LEU* 4.0 22.7 - - + -
243B ALA* 4.2 12.8 - - + -
324B VAL* 4.0 24.9 - - + -
325B PHE 2.8 5.9 + - - -
326B ILE* 3.3 16.8 - - + -
327B LEU* 2.7 26.7 + - - +
329B TYR* 4.8 0.7 - - - -
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Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP 4.4 0.4 + - - -
56B GLY* 4.4 3.2 - - - -
57B PRO* 4.9 4.9 - - - +
60B MET* 3.4 35.6 - - - +
205B LEU* 1.3 76.5 - - - +
207B ALA* 1.3 60.9 + - - +
208B LEU 4.4 0.2 + - - -
326B ILE* 4.5 3.8 - - - +
327B LEU 3.4 6.7 - - - -
329B TYR* 3.5 8.5 - - - -
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLY* 1.3 74.8 - - - +
208B LEU* 1.3 63.6 + - - +
326B ILE* 3.8 19.9 - - + +
327B LEU 2.9 10.0 + - - +
328B ASP* 3.8 14.0 - - + +
329B TYR* 3.0 27.3 + - - +
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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