Contacts of the strand formed by residues 395 - 401 (chain v) in PDB entry 6FF7
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 395 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331v ASP* 5.3 12.8 - - + +
359v TYR* 3.9 22.7 - - + -
360v GLN 3.5 7.2 - - - +
361v ILE* 5.6 0.9 - - - -
362v ALA* 5.3 2.0 - - - -
392v LEU* 3.4 28.3 - - + +
393v LYS 4.4 2.0 - - - +
394v ASN* 1.3 79.4 + - + +
396v VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 396 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359v TYR* 3.4 7.6 - - - -
360v GLN* 3.3 32.5 + - + +
362v ALA* 5.3 6.5 - - + +
392v LEU* 5.4 2.5 - - - -
395v LEU* 1.3 74.3 - - - +
397v LEU* 1.3 67.5 + - - +
398v VAL* 3.3 3.9 + - - +
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Residues in contact with LEU 397 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358v LEU 4.8 1.3 - - - -
359v TYR* 5.1 1.8 - - - +
396v VAL* 1.3 73.1 - - - +
398v VAL* 1.3 60.9 + - - +
399v ASP 6.5 0.2 - - - -
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Residues in contact with VAL 398 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48v GLY* 4.6 19.4 - - - +
358v LEU* 3.3 16.8 + - + +
359v TYR 4.8 0.9 - - - -
360v GLN* 4.6 13.7 - - + +
396v VAL 3.3 5.1 + - - +
397v LEU* 1.3 75.6 - - - +
399v ASP* 1.3 63.0 + - + +
400v GLU 4.4 0.2 + - - -
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Residues in contact with ASP 399 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48v GLY 3.8 16.4 - - - +
49v LYS* 4.7 7.9 - - - -
50v VAL* 4.9 11.4 - - + +
357v TYR* 3.4 6.1 - - - +
358v LEU* 2.9 49.2 + - + +
398v VAL* 1.3 77.9 + - - +
400v GLU* 1.3 61.0 + - - +
401v LEU* 3.8 3.6 - - + +
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Residues in contact with GLU 400 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355v ASN* 5.3 7.0 - - + -
356v HIS 3.6 6.5 - - - +
357v TYR* 4.8 1.3 - - + +
398v VAL 4.4 0.4 + - - -
399v ASP* 1.3 71.6 - - - +
401v LEU* 1.3 64.7 + - - +
402v ASP* 3.3 5.9 + - - +
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Residues in contact with LEU 401 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50v VAL* 5.7 9.6 - - + -
355v ASN* 3.3 5.8 - - - +
356v HIS* 2.9 53.7 + - + +
357v TYR* 5.5 0.9 - - - -
399v ASP* 3.8 4.3 + - + +
400v GLU* 1.3 70.8 - - - +
402v ASP* 1.3 65.5 + - - +
403v SER* 4.4 0.2 - - - -
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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