Contacts of the strand formed by residues 374 - 380 (chain D) in PDB entry 3VI4
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 THR 374 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C PRO* 5.7 11.0 - - + -
315C ASP* 6.0 1.6 - - - +
369D LEU* 4.3 2.7 - - - -
372D GLY 4.0 3.5 + - - +
373D VAL* 1.3 80.5 - - - +
375D ILE* 1.3 63.9 + - - +
410D ILE* 3.3 9.0 - - - +
411D THR* 2.9 45.9 + - - -
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Residues in contact with ILE 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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314C PRO 5.2 4.9 + - - +
315C ASP* 3.9 27.7 - - - +
366D ASN* 4.1 3.8 - - - +
369D LEU* 3.8 20.4 - - + +
374D THR* 1.3 77.9 - - - +
376D SER* 1.3 64.4 + - - +
377D TYR* 3.5 39.1 - - + +
393D ARG* 4.5 2.8 + - - +
408D ILE* 3.7 18.4 - - + -
409D SER 3.3 11.4 - - - +
410D ILE* 3.8 7.2 - - + -
423D PHE* 4.1 24.9 - - + -
425D ILE* 4.4 1.6 - - + -
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Residues in contact with SER 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375D ILE* 1.3 76.6 - - - +
377D TYR* 1.3 64.5 + - - +
407D GLU 3.8 1.0 - - - +
408D ILE* 3.4 5.4 - - - +
409D SER* 2.7 58.4 + - - -
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Residues in contact with TYR 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D LEU* 4.1 22.9 - - + -
365D GLU 4.1 0.5 - - - -
366D ASN* 2.6 34.1 + - - +
375D ILE* 3.5 23.4 - - + +
376D SER* 1.3 81.1 - - - +
378D LYS* 1.3 64.2 + - - +
388D THR* 4.3 0.2 - - - -
389D GLY 3.7 20.6 + - - +
392D GLY* 3.2 31.7 - - - +
393D ARG* 3.2 52.8 + - + +
406D PHE* 5.1 0.9 - + - -
407D GLU 3.7 3.4 - - - -
408D ILE* 3.7 31.6 - - + +
425D ILE* 3.8 9.0 - - + +
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Residues in contact with LYS 378 (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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377D TYR* 1.3 76.9 - - - +
379D SER* 1.3 59.8 + - - +
380D TYR* 4.0 23.6 + - + +
387D GLY 3.7 13.0 - - - +
388D THR* 4.2 17.7 - - + -
392D GLY 3.2 4.6 - - - +
405D GLN 4.1 0.2 - - - +
406D PHE* 3.3 5.0 - - - +
407D GLU* 2.8 57.3 + - + +
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Residues in contact with SER 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D LYS* 1.3 73.7 - - - +
380D TYR* 1.3 66.2 + - - +
381D CYS* 3.9 3.0 - - - -
386D ASN* 3.2 10.2 - - - +
387D GLY* 2.9 41.7 + - - +
391D ASN 3.1 8.3 + - - -
392D GLY 3.1 16.3 + - - -
394D LYS 3.0 27.3 + - - -
395D CYS* 4.0 4.3 - - - -
405D GLN 3.7 2.9 - - - -
406D PHE* 3.7 12.3 - - - -
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Residues in contact with TYR 380 (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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378D LYS* 4.0 27.3 + - + +
379D SER* 1.3 76.7 - - - +
381D CYS* 1.3 65.5 + - - +
386D ASN* 3.4 24.9 - - + +
387D GLY 6.0 0.2 - - - -
395D CYS* 4.0 0.7 - - - -
403D GLU 5.1 0.2 - - - +
404D VAL* 3.6 5.4 - - - +
405D GLN* 2.8 55.4 + - + +
406D PHE 5.0 0.2 - - - -
407D GLU* 3.5 48.6 + - + -
503D NAG 3.5 31.2 - - - -
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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