Contacts of the strand formed by residues 248 - 253 (chain D) in PDB entry 2V90
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 ARG 248 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D PRO* 1.3 80.2 - - - +
249D CYS* 1.3 61.8 + - - +
250D LEU* 3.2 27.0 + - + +
289D ALA 4.3 0.6 + - - -
290D GLY* 3.1 37.4 + - - -
292D GLN* 4.4 6.6 - - - +
295D ASP* 4.4 4.6 + - - -
326D LEU 3.5 1.6 - - - +
327D THR* 3.3 4.1 - - - -
328D VAL* 2.8 42.1 + - + +
330D ASP* 2.9 40.3 + - - +
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Residues in contact with CYS 249 (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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248D ARG* 1.3 72.0 - - - +
250D LEU* 1.3 68.1 + - - +
251D HIS* 3.8 22.7 + - + -
325D SER* 2.9 29.6 - - - -
326D LEU 3.5 4.0 - - - -
327D THR* 3.9 20.3 - - + +
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Residues in contact with LEU 250 (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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248D ARG* 3.2 39.5 - - + +
249D CYS* 1.3 82.6 - - - +
251D HIS* 1.3 64.4 + - - +
252D LEU* 3.7 15.1 - - + +
289D ALA 3.8 15.3 - - - +
291D MET* 3.0 39.5 - - + +
325D SER* 3.3 5.0 + - - -
326D LEU 2.7 39.3 + - - +
328D VAL* 3.5 27.6 - - + -
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Residues in contact with HIS 251 (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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249D CYS* 3.8 26.6 + - + -
250D LEU* 1.3 75.0 - - - +
252D LEU* 1.3 61.4 + - - +
253D GLU* 4.3 2.2 + - - +
289D ALA* 4.1 13.5 + - - +
324D VAL 3.7 4.3 - - - -
325D SER* 3.7 20.9 + - - -
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Residues in contact with LEU 252 (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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250D LEU* 3.7 31.0 - - + +
251D HIS* 1.3 78.8 - - - +
253D GLU* 1.3 64.6 + - - +
254D LYS 4.1 0.2 - - - -
259D PHE* 3.9 30.0 - - + -
261D PHE* 4.3 0.4 - - + -
285D PRO* 4.7 5.2 - - + -
286D ALA* 3.8 18.6 - - + +
289D ALA* 4.3 13.2 - - + -
291D MET* 3.5 24.2 - - - -
322D SER 4.0 0.3 - - - +
323D CYS* 3.4 5.7 - - - +
324D VAL* 2.9 39.5 + - + +
326D LEU* 3.9 22.9 - - + -
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Residues in contact with GLU 253 (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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251D HIS 4.3 2.4 + - - +
252D LEU* 1.3 76.0 - - - +
254D LYS* 1.3 66.1 + - - +
259D PHE* 4.1 1.8 - - - -
285D PRO* 3.1 25.4 - - - +
322D SER 3.5 4.3 - - - +
323D CYS* 4.1 18.8 - - + -
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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