Contacts of the strand formed by residues 372 - 375 (chain D) in PDB entry 3EI4
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 372 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352D VAL* 4.6 8.7 - - + -
353D VAL 3.5 7.0 - - - +
370D ARG 4.2 0.9 + - - +
371D THR* 1.3 70.1 + - - +
373D ASP* 1.3 67.1 + - - +
374D VAL* 4.6 2.2 - - + +
384D CYS 3.8 0.9 - - - +
385D GLN* 3.2 4.5 - - - -
386D LEU* 2.7 54.5 + - + +
392D SER* 6.0 0.4 - - - +
395D SER* 3.7 19.7 - - - +
398D ASN* 3.4 21.1 - - - +
407D LEU* 4.0 16.8 - - + -
409D SER* 3.3 27.6 - - - +
411D MET* 5.7 1.3 - - + -
418D TRP* 3.5 27.8 - - + +
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Residues in contact with ASP 373 (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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329D HIS* 2.9 16.3 - - - -
351D ILE 3.4 0.6 - - - +
352D VAL* 3.3 5.9 - - - +
353D VAL* 2.7 42.9 + - + +
355D ARG* 2.7 38.5 + - - +
371D THR* 3.2 17.0 - - - +
372D ILE* 1.3 72.6 - - - +
374D VAL* 1.3 61.7 + - - +
375D PHE* 3.8 19.8 - - + -
382D MET* 4.2 3.8 - - - +
385D GLN* 2.6 31.2 + - - +
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Residues in contact with VAL 374 (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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95D LEU* 4.3 13.5 - - + -
98D LEU* 3.9 24.0 - - + -
350D LEU* 4.0 32.5 - - + -
351D ILE 3.0 8.3 - - - +
352D VAL* 3.8 19.1 - - + -
372D ILE* 4.6 8.1 - - + +
373D ASP* 1.3 78.1 - - - +
375D PHE* 1.3 57.0 + - - +
382D MET* 3.6 2.5 - - - -
383D MET* 2.6 34.1 + - - +
384D CYS* 2.8 23.7 + - - +
386D LEU* 5.3 4.3 - - + -
400D PHE* 5.3 3.8 - - + -
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Residues in contact with PHE 375 (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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312D ILE* 4.5 2.5 - - + -
327D ILE* 3.6 41.1 - - + -
328D PRO 4.7 2.7 - - - -
329D HIS* 3.9 22.4 - + + -
350D LEU* 3.5 7.6 - - - +
351D ILE* 2.8 42.9 + - + -
353D VAL* 3.7 31.4 - - + -
355D ARG* 4.7 3.1 - - - -
373D ASP* 3.8 8.3 - - + -
374D VAL* 1.3 75.7 - - - +
376D ASP* 1.3 63.0 + - - +
380D GLY 3.7 13.2 - - - -
381D LYS 3.9 2.9 - - - +
382D MET* 3.2 47.8 - - + -
383D MET* 4.1 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
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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