Contacts of the strand formed by residues 234 - 242 (chain B) in PDB entry 1D2G
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 GLY 234 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B GLN* 3.2 6.1 - - - +
224B VAL* 2.6 42.9 + - - -
227B ALA* 3.8 16.5 - - - +
228B GLY* 3.8 6.3 - - - +
233B PRO* 1.3 75.6 - - - +
235B PHE* 1.3 64.5 + - - -
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Residues in contact with PHE 235 (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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25B GLU* 4.8 3.9 - - - +
199B THR* 6.1 0.4 - - + -
221B THR* 4.4 20.9 - - + -
222B VAL 3.4 4.3 - - - +
223B GLN* 3.3 50.3 - - + -
224B VAL* 4.2 0.6 - - - +
233B PRO* 4.1 16.2 - - + -
234B GLY* 1.3 77.5 - - - -
236B SER* 1.3 60.5 + - - +
237B LYS* 5.2 1.7 - - - +
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 3.2 37.8 + - - +
29B VAL* 3.3 35.2 - - - +
221B THR* 3.4 2.9 - - - -
222B VAL* 2.9 32.1 + - - +
224B VAL* 4.1 7.4 - - - +
235B PHE* 1.3 74.9 - - - +
237B LYS* 1.3 71.4 + - - +
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Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 4.9 2.8 + - - +
26B ALA* 3.6 20.3 + - - +
29B VAL* 3.7 3.2 - - - +
219B ASP* 3.6 32.5 + - - +
220B TYR 3.0 11.5 + - - +
221B THR* 3.4 27.8 - - + +
235B PHE 5.2 1.6 - - - +
236B SER* 1.3 84.0 + - - +
238B PHE* 1.3 69.8 + - - +
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Residues in contact with PHE 238 (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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9A SER* 3.6 11.7 - - - +
12A VAL* 4.2 12.8 - - + -
26B ALA* 3.9 18.8 - - + +
29B VAL* 4.3 6.7 - - + -
30B TRP* 4.2 18.2 - + + -
33B TYR* 3.4 48.7 - + + -
219B ASP* 3.7 4.4 - - - +
220B TYR* 2.9 68.5 + + + -
222B VAL* 4.1 10.8 - - + -
237B LYS* 1.3 80.2 - - - +
239B ARG* 1.3 69.9 + - - +
240B LEU* 4.0 17.0 - - + -
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Residues in contact with ARG 239 (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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4A VAL 5.4 0.2 + - - -
5A TYR* 3.1 40.6 - - - +
6A ARG* 2.8 48.1 + - - +
7A THR 3.5 10.8 - - - +
8A ARG* 3.3 6.4 - - - +
9A SER* 3.0 33.8 + - - +
12A VAL* 3.9 4.3 - - - +
205B SER* 5.1 2.2 + - - -
217B THR* 3.4 21.1 - - + +
218B LEU 3.4 5.2 - - - +
219B ASP* 3.0 35.3 + - - +
238B PHE* 1.3 79.2 - - - +
240B LEU* 1.3 67.3 + - - +
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Residues in contact with LEU 240 (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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7A THR 3.8 3.1 - - - -
8A ARG* 4.0 15.7 - - + -
12A VAL* 4.1 11.9 - - + -
13A ALA 4.2 17.0 - - - +
14A ALA* 4.4 15.5 - - + -
30B TRP* 5.1 2.7 - - + +
33B TYR* 4.5 13.7 - - + +
142B HIS* 5.4 5.4 - - + +
217B THR* 3.7 1.7 - - - +
218B LEU* 2.8 30.5 + - - +
220B TYR* 3.9 14.1 - - + -
238B PHE* 4.0 19.5 - - + -
239B ARG* 1.3 81.4 - - - +
241B SER* 1.3 64.8 + - - +
242B TYR* 3.8 26.8 - - + +
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Residues in contact with SER 241 (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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7A THR* 2.7 38.6 + - - +
8A ARG* 4.7 1.6 - - - +
141B ALA 4.2 2.9 - - - +
142B HIS* 4.3 14.3 - - - +
215B MET* 3.8 17.9 - - - -
216B VAL 3.6 4.0 - - - -
217B THR* 2.6 27.6 + - - -
240B LEU* 1.3 75.0 - - - +
242B TYR* 1.3 72.5 + - - +
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Residues in contact with TYR 242 (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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33B TYR* 4.5 3.8 + - - -
138B ASN* 3.6 26.5 - - - -
141B ALA* 3.1 13.0 - - + +
142B HIS* 3.7 33.5 + + - -
144B PRO* 6.3 0.4 - - - -
177B TYR* 3.4 22.4 - + + +
215B MET* 3.6 6.2 - - - +
216B VAL* 3.0 41.6 + - + +
218B LEU* 3.7 25.4 - - + -
220B TYR* 2.6 25.2 + - - -
240B LEU* 3.8 32.6 - - + +
241B SER* 1.3 77.1 - - - +
243B TYR* 1.3 61.4 + - - +
244B PRO* 3.7 0.3 - - - +
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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