Contacts of the strand formed by residues 262 - 267 (chain D) in PDB entry 1D2H
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 CYS 262 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D GLN* 4.0 25.6 + - - -
258D PHE* 3.2 41.7 - - + -
260D GLY 3.2 8.1 + - - +
261D ARG* 1.3 79.3 - - - +
263D GLN* 1.3 65.6 + - - +
264D HIS 4.5 0.9 - - - -
288D LEU* 4.2 7.2 - - - -
289D LYS 3.2 4.7 - - - +
290D LYS* 3.5 15.7 - - - -
291D THR* 3.0 21.1 + - - -
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Residues in contact with GLN 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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262D CYS* 1.3 80.7 - - - +
264D HIS* 1.3 61.9 + - - +
265D SER* 4.0 4.5 + - - -
287D VAL* 3.4 5.7 - - - +
288D LEU* 4.4 0.7 - - - -
289D LYS* 3.0 42.7 + - + +
291D THR* 2.6 41.2 + - - +
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Residues in contact with HIS 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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251D THR* 3.6 17.6 - - + +
254D VAL* 3.3 26.1 - - + +
255D GLN* 3.1 34.2 + - - +
262D CYS* 4.1 1.6 - - - -
263D GLN* 1.3 72.2 - - - +
265D SER* 1.3 87.0 + - - +
266D VAL* 3.5 18.5 - - + +
286D HIS* 2.8 41.8 + + + -
287D VAL 3.4 5.6 - - - -
288D LEU* 3.4 14.9 - - + +
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Residues in contact with SER 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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263D GLN 4.0 4.9 + - - -
264D HIS* 1.3 88.1 + - - +
266D VAL* 1.3 61.4 + - - +
267D LEU* 5.6 0.9 - - - -
287D VAL* 2.8 51.9 + - - +
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Residues in contact with VAL 266 (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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247D LEU* 3.7 28.7 - - + -
251D THR* 4.6 4.9 - - + +
264D HIS* 3.5 17.5 - - + +
265D SER* 1.3 74.4 - - - +
267D LEU* 1.3 76.6 + - - +
272D PRO* 5.2 0.3 - - - +
273D TYR* 3.7 27.4 + - + +
284D PHE* 4.0 11.4 - - + -
285D ILE 3.1 7.2 - - - +
286D HIS* 4.0 17.0 - - + +
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Residues in contact with LEU 267 (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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47D TRP* 3.7 31.6 - - + +
51D LEU* 5.5 0.9 - - + -
265D SER* 4.0 1.6 - - - +
266D VAL* 1.3 83.3 - - - +
268D GLY* 1.3 66.2 + - - +
270D PHE* 3.9 24.7 - - + +
271D LYS 3.4 18.2 - - - +
272D PRO* 5.2 1.1 - - + -
273D TYR* 3.8 2.2 - - - +
283D TYR 4.6 0.2 - - - -
284D PHE* 3.5 2.6 - - - -
285D ILE* 2.8 51.9 + - + +
287D VAL* 3.6 23.6 - - + -
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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
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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