Contacts of the strand formed by residues 289 - 292 (chain C) in PDB entry 2X1L
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 ILE 289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C PHE* 2.8 54.2 + - + +
186C ILE* 3.5 2.6 - - - +
187C GLY 2.8 26.5 + - - +
260C HIS* 3.5 26.7 - - + +
262C ILE* 3.7 32.1 - - + -
267C ILE* 5.1 2.7 - - + -
270C HIS* 4.0 17.7 - - + +
271C THR* 3.9 17.9 - - + -
286C PRO* 3.9 16.4 - - + -
288C ARG* 1.3 77.5 - - - +
290C PHE* 1.3 60.9 + - - +
291C ALA 4.9 0.7 - - - +
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Residues in contact with PHE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C GLY* 3.4 8.7 - - - -
188C PRO* 3.6 28.0 - - + -
259C LEU* 3.9 19.2 - - + +
260C HIS 3.0 9.7 + - - +
261C MET* 3.7 7.8 - - - +
262C ILE* 3.1 27.5 + - - +
288C ARG* 3.5 28.9 - - - +
289C ILE* 1.3 72.2 - - - +
291C ALA* 1.3 74.0 + - - +
292C HIS* 3.8 0.3 + - - -
334C PHE* 3.4 51.8 - + - -
335C GLY* 4.0 6.7 - - - -
406C VAL* 4.1 1.1 - - + -
407C PRO* 3.6 24.7 - - + -
603C 2HP 4.1 7.9 - - - -
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLY 3.0 11.1 + - - +
188C PRO* 3.5 18.9 - - - +
191C ARG* 4.4 6.9 - - + -
262C ILE* 3.1 9.9 - - + -
263C GLY 3.9 4.3 - - - +
264C LYS* 3.8 28.8 - - + +
267C ILE* 3.9 24.9 - - + -
289C ILE* 4.2 0.8 - - - +
290C PHE* 1.3 75.4 - - - +
292C HIS* 1.3 62.6 + - - +
335C GLY* 4.0 4.5 - - - +
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Residues in contact with HIS 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C TYR* 3.8 15.3 - + + -
25C GLU* 2.7 46.5 + - + +
261C MET* 5.2 2.7 - - + -
262C ILE* 2.8 29.0 + - - -
263C GLY* 3.8 10.3 - - - -
264C LYS* 3.2 25.6 + - - +
290C PHE* 3.8 4.6 + - - -
291C ALA* 1.3 73.9 - - - +
293C GLY* 1.3 78.8 + - - +
334C PHE* 3.6 36.8 - + + -
335C GLY* 4.0 7.6 - - - -
601C ADN 3.3 30.5 - + - -
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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