Contacts of the strand formed by residues 361 - 365 (chain D) in PDB entry 1EQB
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 361 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D VAL 3.1 13.9 - - - -
323D LEU* 4.1 6.7 - - - -
330D GLY* 3.2 17.2 - - - +
347D ASN 2.9 32.1 + - - +
349D VAL* 4.0 5.6 - - - -
359D THR 3.5 1.4 - - - -
360D SER* 1.3 80.9 - - - +
362D ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 362 (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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302D PHE* 5.1 1.1 - - + -
319D PHE 4.1 0.5 - - - +
320D LEU* 3.6 3.7 - - - +
321D VAL* 3.0 50.7 + - + +
323D LEU* 4.1 3.8 - - + -
330D GLY 4.1 7.9 - - - +
333D ALA* 3.6 28.3 - - + -
334D ASP 4.4 3.8 - - - +
337D LEU* 4.0 23.3 - - + -
344D VAL* 4.6 11.0 - - + -
345D ASN 3.6 10.5 - - - +
346D LYS* 4.7 0.7 - - - -
347D ASN* 4.1 4.3 - - - +
349D VAL* 5.2 0.6 - - - +
361D GLY* 1.3 80.8 - - - +
363D ARG* 1.3 59.3 + - - +
364D VAL* 4.2 17.7 + - + -
386D MET* 4.4 6.7 - - + -
390D LEU* 4.7 13.5 - - + -
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Residues in contact with ARG 363 (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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65C PHE* 4.0 2.6 - - - -
32D LEU 3.7 8.2 - - - +
33D ILE* 4.2 1.2 - - - +
34D ALA* 3.8 21.5 - - + +
35D SER* 3.5 15.6 + - - +
175D SER 2.8 30.6 + - - -
176D ALA* 4.0 9.6 - - + -
203D HIS* 3.6 2.6 + - - -
318D LEU* 4.3 6.7 - - + -
319D PHE 3.7 7.0 - - - +
320D LEU* 3.7 15.0 - - + -
344D VAL* 4.0 13.5 - - - +
345D ASN* 3.1 35.5 + - - +
347D ASN* 3.5 23.0 + - + +
362D ILE* 1.3 72.3 - - - +
364D VAL* 1.3 70.3 + - - +
4292D GLY* 2.8 38.2 + - - -
4293D FFO 3.8 13.9 + - - -
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Residues in contact with VAL 364 (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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32D LEU* 3.5 31.4 - - + -
34D ALA* 4.4 2.5 - - - -
298D MET* 4.4 10.1 - - + -
302D PHE* 5.1 0.7 - - + -
318D LEU* 3.1 7.6 - - - +
319D PHE* 3.0 73.4 + - + +
321D VAL* 4.8 1.1 - - + -
344D VAL* 4.6 2.9 - - + -
362D ILE* 4.3 24.0 - - + +
363D ARG* 1.3 81.2 - - - +
365D GLY* 1.3 63.6 + - - +
386D MET* 4.3 12.6 - - + -
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Residues in contact with GLY 365 (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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31D GLU 4.3 2.3 - - - +
32D LEU* 2.8 37.9 + - - +
33D ILE 5.0 0.8 - - - +
34D ALA* 3.8 22.3 - - - +
317D HIS 3.3 9.4 - - - -
364D VAL* 1.3 76.4 - - - +
366D THR* 1.3 62.2 + - - -
367D PRO* 3.2 6.1 - - - -
368D ALA* 5.0 1.0 + - - +
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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