Contacts of the strand formed by residues 259 - 262 (chain X) in PDB entry 3EXG
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 LEU 259 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207X ILE* 4.3 0.8 - - - +
208X THR* 3.3 32.8 - - + +
210X VAL* 3.8 18.8 - - + -
249X ILE* 4.2 3.8 - - + -
253X VAL* 3.9 11.9 - - + -
258X HIS* 1.3 76.0 - - - +
260X VAL* 1.3 73.4 + - - +
261X THR* 4.7 4.7 - - + -
275X ILE* 4.5 12.1 - - + +
276X CYS* 5.6 0.7 - - - -
279X ILE* 3.2 40.8 - - + -
288X LEU* 4.5 6.7 - - + +
290X ALA 5.5 0.8 + - - -
291X PRO 4.6 1.2 - - - +
292X ALA* 3.5 22.2 - - + +
293X VAL* 3.2 20.8 + - - +
326X THR* 4.7 3.2 - - - +
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Residues in contact with VAL 260 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207X ILE* 3.8 21.8 - - + -
208X THR 3.0 8.9 + - - +
209X VAL* 3.4 7.5 - - + +
210X VAL 2.8 25.1 + - - -
259X LEU* 1.3 81.6 - - - +
261X THR* 1.3 74.2 + - - +
262X VAL* 4.4 11.2 - - + -
293X VAL* 3.3 29.4 - - + +
295X VAL* 4.5 12.1 - - + -
319X ILE* 5.3 2.2 - - + -
322X ALA* 4.4 5.2 - - + +
323X ILE* 4.1 21.5 - - + -
326X THR* 3.9 5.6 - - - +
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Residues in contact with THR 261 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210X VAL* 3.3 8.7 - - + -
259X LEU* 4.7 8.7 - - + -
260X VAL* 1.3 78.5 - - - +
262X VAL* 1.3 60.3 + - - +
263X GLU* 5.0 2.2 + - - +
272X GLY* 3.5 17.1 - - - +
275X ILE* 3.6 39.3 - - + -
276X CYS* 4.7 8.5 - - - -
292X ALA* 6.1 0.2 - - + -
293X VAL 2.8 10.3 + - - +
294X ARG* 3.3 24.4 - - - +
295X VAL* 2.6 36.2 + - - +
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Residues in contact with VAL 262 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209X VAL* 3.9 13.9 - - + -
210X VAL 2.7 10.3 + - - -
211X SER* 2.7 35.3 + - - +
212X HIS* 4.0 1.9 + - - -
215X PRO* 3.8 19.1 - - + -
219X CYS* 3.7 21.1 - - - -
238X MET* 5.5 0.7 - - - +
260X VAL* 4.4 6.1 - - + -
261X THR* 1.3 79.4 - - - +
263X GLU* 1.3 65.4 + - - +
295X VAL* 3.1 12.6 - - + +
314X PRO* 4.1 13.0 - - + -
319X ILE* 3.6 33.2 - - + -
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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