Contacts of the strand formed by residues 301 - 305 (chain D) in PDB entry 1OFG
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 ILE 301 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D MET* 3.9 37.9 - - + +
166D ALA* 4.0 9.6 - - + -
167D ALA* 3.9 16.6 - - + +
170D LEU* 4.0 20.2 - - + -
288D LEU* 4.0 7.9 - - + -
289D LEU 3.3 6.1 - - - +
290D MET* 3.7 25.1 - - + -
292D PRO 5.5 0.9 - - - +
299D ASN* 5.9 0.4 - - + -
300D LEU* 1.3 81.4 - - - +
302D SER* 1.3 62.8 + - - +
303D VAL* 5.9 1.8 - - + -
310D ASN 3.9 0.2 - - - +
311D GLN* 3.3 5.7 - - - +
312D SER* 3.0 53.5 + - - +
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Residues in contact with SER 302 (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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287D VAL 3.6 0.9 - - - +
288D LEU* 3.4 2.6 - - - -
289D LEU* 2.7 49.5 + - - +
300D LEU* 5.7 2.9 - - - -
301D ILE* 1.3 77.9 - - - +
303D VAL* 1.3 64.5 + - - +
304D GLN* 3.6 25.2 + - - +
309D ALA* 4.0 9.5 - - - +
310D ASN 3.4 7.8 + - - -
311D GLN* 4.0 20.3 + - - -
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Residues in contact with VAL 303 (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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170D LEU* 4.1 30.7 - - + -
175D GLN* 4.8 12.3 - - + +
176D LEU* 4.1 7.4 - - + -
286D ALA* 3.9 24.9 - - + -
287D VAL 3.4 5.4 - - - +
288D LEU* 4.3 9.0 - - + -
301D ILE* 5.8 2.2 - - + -
302D SER* 1.3 75.3 + - - +
304D GLN* 1.3 63.8 + - - +
305D THR* 4.3 3.4 + - + -
308D HIS* 3.9 1.7 - - - +
309D ALA* 3.4 1.6 - - - -
310D ASN* 2.8 51.6 + - + +
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Residues in contact with GLN 304 (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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274C THR* 5.9 0.3 - - - -
275C THR 5.6 3.1 - - - +
278C ARG* 2.8 28.0 + - - +
291C ASP* 3.6 19.3 + - - +
286D ALA* 3.8 1.1 - - - +
287D VAL* 2.8 45.5 + - + +
289D LEU* 4.0 15.5 - - + +
302D SER* 3.6 23.0 + - - +
303D VAL* 1.3 77.6 - - - +
305D THR* 1.3 68.7 + - - +
308D HIS 3.4 9.6 - - - +
309D ALA* 4.6 7.7 - - + +
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Residues in contact with THR 305 (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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313B MET* 5.2 0.7 - - - +
316B GLN* 5.6 1.7 + - - -
274C THR* 6.2 1.3 - - + -
285D LYS 3.7 22.7 - - - +
286D ALA* 3.8 10.3 - - + -
303D VAL* 5.3 3.7 + - + -
304D GLN* 1.3 79.7 - - - +
306D PRO* 1.3 72.7 - - + +
307D GLY 3.2 0.7 + - - -
308D HIS* 2.7 50.4 + - - +
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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