Contacts of the strand formed by residues 261 - 265 (chain D) in PDB entry 1I2M
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 261 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253D PHE* 4.1 6.3 - - + -
254D ALA 3.6 5.8 - - - +
255D ILE* 4.7 6.3 - - + -
259D GLY 4.2 5.8 - - - +
260D HIS* 1.3 74.6 - - - +
262D TYR* 1.3 70.6 + - - +
285D ASN* 3.3 7.0 + - - +
286D LEU* 2.8 43.5 + - + +
289D PHE* 3.9 18.3 + - + +
296D TRP* 3.9 27.6 - - + -
299D PHE* 3.7 37.5 - - + -
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Residues in contact with TYR 262 (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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231D LEU* 3.8 31.2 - - + -
232D LYS 5.5 2.7 - - - -
240D VAL* 4.1 21.6 - - + +
242D PHE* 3.9 23.8 - + + -
253D PHE* 3.3 4.2 - - - +
254D ALA* 2.8 38.1 + - + +
256D SER* 3.9 12.6 - - - -
258D GLU* 5.6 1.4 + - - -
260D HIS* 3.7 34.4 + - + -
261D VAL* 1.3 82.4 - - - +
263D GLY* 1.3 59.2 + - - +
264D PHE* 5.1 2.2 - - + -
283D PRO* 4.4 7.0 - - + -
284D GLN 3.2 8.1 - - - -
285D ASN* 3.7 38.4 + - + +
286D LEU* 4.1 3.4 - - - -
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Residues in contact with GLY 263 (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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252D THR 3.1 11.4 - - - -
253D PHE* 4.4 0.4 - - - -
262D TYR* 1.3 76.7 - - - +
264D PHE* 1.3 65.9 + - - +
272D LEU* 4.0 9.4 - - - -
280D CYS* 4.3 1.4 - - - +
282D ILE 4.0 0.5 - - - +
283D PRO* 3.6 0.2 - - - +
284D GLN* 2.9 37.8 + - - +
286D LEU* 3.8 16.1 - - - +
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Residues in contact with PHE 264 (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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193D LEU* 4.0 21.3 - - + -
195D THR* 4.7 4.5 - - + -
202D GLY 3.9 1.6 - - - +
203D GLN* 3.1 29.1 - - - -
204D LEU 3.7 10.5 - - - -
205D GLY* 3.5 15.3 - - - -
229D VAL* 4.3 11.2 - - + -
242D PHE* 6.1 1.8 - + - -
251D PHE* 3.4 2.6 - - - +
252D THR* 2.8 61.5 + - + +
254D ALA* 5.0 8.1 - - + -
262D TYR* 5.5 1.1 - - + -
263D GLY* 1.3 82.0 - - - +
265D GLY* 1.3 60.8 + - - +
272D LEU* 3.7 9.4 - - - +
280D CYS* 3.4 13.7 - - - +
282D ILE 4.1 1.3 - - - +
283D PRO* 3.7 36.3 - - + -
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Residues in contact with GLY 265 (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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201D GLN 3.1 18.6 - - - -
202D GLY 3.5 11.8 + - - -
203D GLN 3.6 0.7 - - - -
250D TYR 3.6 7.6 - - - -
251D PHE* 4.1 0.2 - - - -
264D PHE* 1.3 75.4 - - - +
266D LEU* 1.3 65.9 + - - -
272D LEU* 3.7 5.5 - - - +
279D SER* 3.5 1.2 - - - -
280D CYS 2.7 36.0 + - - -
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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