Contacts of the strand formed by residues 265 - 270 (chain I) in PDB entry 3STJ
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 ALA 265 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244I ILE* 5.9 0.2 - - + -
247I THR 3.7 4.3 - - - -
249I MET* 4.1 3.3 - - - +
264I GLY* 1.3 72.4 - - - -
266I PHE* 1.3 61.5 + - - +
267I VAL* 3.8 1.7 + - + -
285I ASP 3.7 0.7 - - - +
286I ILE* 3.2 6.1 - - - -
287I ILE* 2.8 55.6 + - + +
295I LEU* 5.3 0.6 - - + +
298I PHE* 3.3 34.5 - - + -
301I LEU* 4.3 10.8 - - + -
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Residues in contact with PHE 266 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I GLY* 3.1 6.3 - - - -
247I THR* 2.9 54.2 + - - +
248I GLU 4.5 3.8 - - - +
249I MET* 3.6 31.7 - - + +
253I ILE* 4.2 24.9 - - + -
257I PHE* 4.9 10.5 - + - -
265I ALA* 1.3 72.7 - - - +
267I VAL* 1.4 66.9 + - - +
268I SER* 3.6 10.4 + - - -
284I GLY* 4.0 28.0 - - - -
285I ASP 3.8 1.1 - - - -
286I ILE* 3.9 10.5 - - + -
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Residues in contact with VAL 267 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I ILE* 3.7 32.8 - - + -
245I LYS 3.8 5.2 - - - +
246I GLY* 4.5 0.9 - - - -
265I ALA* 4.5 2.2 - - + +
266I PHE* 1.4 76.2 - - - +
268I SER* 1.3 59.6 - - - +
269I GLU 3.8 13.2 - - - +
270I VAL* 3.8 13.0 - - + -
281I VAL* 4.7 2.5 - - + -
282I LYS 4.1 11.0 - - - +
283I ALA* 4.2 1.1 - - - -
284I GLY* 2.7 31.4 + - - -
285I ASP* 2.8 27.0 + - + +
287I ILE* 3.7 33.4 - - + -
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Residues in contact with SER 268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245I LYS* 2.9 23.8 + - - +
246I GLY* 3.9 6.3 - - - -
247I THR* 5.5 3.9 - - - +
266I PHE* 3.6 14.0 + - - -
267I VAL* 1.3 72.8 - - - +
269I GLU* 1.3 65.3 + - - +
283I ALA* 3.4 16.8 - - - +
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Residues in contact with GLU 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I ILE* 3.5 3.6 - - - -
245I LYS* 2.8 72.9 + - + +
267I VAL* 3.7 3.5 - - - +
268I SER* 1.3 82.6 - - - +
270I VAL* 1.3 70.6 + - - +
271I LEU* 3.5 21.7 + - + +
283I ALA* 4.5 3.6 - - - -
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Residues in contact with VAL 270 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243I GLY 3.6 2.7 - - - +
244I ILE* 3.7 14.1 - - + -
267I VAL* 3.8 3.1 - - + -
269I GLU* 1.3 79.9 - - - +
271I LEU* 1.3 66.9 + - - +
272I PRO* 3.5 7.1 - - - +
276I SER* 3.8 13.5 - - - -
277I ALA* 3.6 32.4 - - + +
281I VAL 3.2 28.7 - - - +
282I LYS* 3.8 3.6 - - - -
283I ALA* 3.7 23.8 - - + +
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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
------------------------------------------------------------
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