Contacts of the strand formed by residues 318 - 322 (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 LEU 318 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ALA* 3.8 16.8 - - + -
174D PHE* 5.4 1.1 - - + -
175D SER 3.6 25.1 - - - +
176D ALA* 4.2 6.7 - - - +
177D TYR 3.5 33.7 - - - +
178D SER* 3.3 3.7 - - - -
203D HIS* 3.6 23.6 - - + -
314D THR* 2.7 26.7 + - - -
316D ASN* 2.9 12.4 + - - +
317D HIS* 1.3 88.7 - - + +
319D PHE* 1.3 74.0 + - - +
320D LEU* 5.2 0.7 - - + +
363D ARG* 4.3 7.2 - - + -
364D VAL 3.1 14.4 - - - +
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Residues in contact with PHE 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D SER* 4.2 7.2 - - - -
295D ALA* 3.9 11.2 - - + -
298D MET* 3.8 31.0 - - + -
299D VAL* 3.4 31.0 - - + -
302D PHE* 4.2 18.4 - + - -
309D VAL* 4.2 13.5 - - + -
310D VAL 5.6 0.2 - - - +
314D THR* 4.3 5.4 - - + -
317D HIS 5.6 0.2 - - - -
318D LEU* 1.3 89.0 - - - +
320D LEU* 1.3 65.3 + - - +
321D VAL* 3.6 27.8 - - + -
362D ILE 4.1 0.2 - - - +
363D ARG* 3.7 3.0 - - - +
364D VAL* 3.0 63.0 + - + -
366D THR* 5.4 1.1 - - + -
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D ALA 5.3 2.5 - - - +
123D HIS 6.0 0.9 - - - -
124D GLY* 5.9 1.1 - - - -
176D ALA* 3.7 28.3 - - + +
178D SER* 5.4 1.0 - - - -
309D VAL* 3.3 11.5 - - - +
310D VAL* 3.1 54.9 + - + +
318D LEU* 5.8 0.4 - - + -
319D PHE* 1.3 75.1 - - - +
321D VAL* 1.3 63.1 + - - +
322D ASP 4.0 0.2 - - - -
347D ASN* 3.8 19.3 - - + +
348D SER 4.0 15.9 - - - +
349D VAL* 4.3 11.7 - - + -
350D PRO* 4.5 5.4 - - + -
362D ILE 3.6 3.1 - - - +
363D ARG* 3.7 35.7 - - + -
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Residues in contact with VAL 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D PHE* 3.7 26.2 - - + -
307D TYR* 4.2 17.7 - - + -
308D LYS 3.4 8.1 - - - +
309D VAL* 4.6 4.5 - - + -
319D PHE* 3.6 30.1 - - + -
320D LEU* 1.3 74.4 - - - +
322D ASP* 1.3 60.3 + - - +
323D LEU* 3.5 25.7 + - + +
349D VAL* 4.8 2.0 - - - -
361D GLY* 3.1 25.3 - - - -
362D ILE* 3.0 28.2 + - + +
364D VAL* 4.8 0.4 - - + -
390D LEU* 5.1 0.4 - - + -
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Residues in contact with ASP 322 (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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307D TYR* 5.5 0.7 - - - -
308D LYS* 2.8 60.0 + - + +
310D VAL* 4.4 13.5 - - + +
320D LEU 4.0 1.8 - - - -
321D VAL* 1.3 69.2 - - - +
323D LEU* 1.3 61.6 + - - +
324D VAL* 3.0 33.2 + - - +
325D ASP* 3.5 14.6 + - - +
326D LYS* 5.2 0.9 - - - +
349D VAL* 3.6 26.5 - - - +
350D PRO* 4.7 5.4 - - - +
360D SER 3.9 2.7 - - - -
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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
------------------------------------------------------------
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