Contacts of the strand formed by residues 358 - 364 (chain A) in PDB entry 1DVM
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 PHE 358 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PHE* 4.2 9.0 - + - -
235A MET* 6.0 0.2 - - - -
237A ILE* 4.0 17.0 - - + -
238A ALA 3.7 11.2 - - - +
239A ALA* 4.1 14.4 - - + -
247A LEU* 3.5 14.0 - - - +
275A LEU* 4.5 4.5 - - + -
276A PRO* 4.2 13.9 - - + -
278A PHE* 3.8 33.4 - + - -
354A ILE* 3.3 25.4 - - + -
356A ARG 3.5 9.6 - - - +
357A PRO* 1.3 75.5 - - - +
359A LEU* 1.3 68.5 + - - +
360A PHE* 4.6 9.0 - - + -
375A GLN* 3.5 1.7 - - - -
376A VAL* 2.7 65.8 + - + -
377A MET* 4.2 0.5 - - - +
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 6.0 0.4 - - + -
237A ILE* 3.8 1.6 - - - -
238A ALA* 3.0 48.8 + - + -
247A LEU* 3.4 27.6 - - + +
250A LEU* 4.1 12.1 - - + -
251A THR* 3.4 38.4 - - + +
254A LEU* 5.1 8.1 - - + -
262A TRP* 5.1 3.6 - - + -
358A PHE* 1.3 80.5 - - - +
360A PHE* 1.3 61.9 + - - +
361A VAL* 4.6 17.0 - - + -
373A MET* 6.1 2.0 - - + -
374A GLY 3.1 17.9 - - - +
375A GLN* 4.1 6.7 - - + -
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Residues in contact with PHE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.1 13.7 - - + -
235A MET* 3.5 37.7 - - + -
236A PHE 3.1 12.3 - - - +
237A ILE* 5.0 1.3 - - + -
278A PHE* 4.0 16.6 - + - -
326A ILE* 3.9 25.8 - - + -
358A PHE* 4.6 8.5 - + + -
359A LEU* 1.3 76.3 - - - +
361A VAL* 1.3 73.4 + - - +
362A VAL* 4.0 13.2 - - + -
372A PHE* 4.2 3.6 - - + -
373A MET* 3.3 12.8 - - - +
374A GLY* 3.1 59.7 + - - +
376A VAL* 4.1 18.6 - - + -
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A SER 3.4 2.8 - - - +
236A PHE* 2.7 46.2 + - + -
254A LEU* 3.9 26.5 - - + -
259A ILE* 4.1 26.0 - - + -
262A TRP* 4.9 4.0 - - + -
359A LEU* 4.6 9.9 - - + -
360A PHE* 1.3 81.4 - - - +
362A VAL* 1.3 66.9 + - - +
363A ARG* 4.8 4.9 - - + +
370A VAL* 3.6 27.4 - - + -
372A PHE 3.4 3.8 - - - -
373A MET* 4.2 9.4 - - + -
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PHE* 4.0 32.1 - - + -
228A TYR* 4.4 3.1 - - + -
233A LEU* 4.1 17.0 - - + -
234A SER 3.3 8.7 - - - +
235A MET* 3.7 34.8 - - + -
360A PHE* 4.0 4.3 - - + -
361A VAL* 1.3 74.3 - - - +
363A ARG* 1.3 64.1 + - - +
370A VAL* 3.6 2.3 - - - -
371A LEU* 2.8 26.7 + - + -
372A PHE* 2.7 40.7 + - + +
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Residues in contact with ARG 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A HIS* 5.6 2.6 - - - -
233A LEU* 3.3 8.2 - - - -
234A SER* 3.0 26.1 + - - +
236A PHE* 3.4 29.4 - - + -
256A ALA 5.6 1.4 + - - -
259A ILE* 4.4 15.6 - - + +
260A SER* 4.6 10.9 + - - +
263A LYS* 3.5 39.4 - - - +
361A VAL* 4.9 4.3 - - + +
362A VAL* 1.3 76.0 - - - +
364A HIS* 1.3 58.7 + - - +
365A ASN* 2.8 58.1 + - - +
368A GLY* 3.3 29.9 - - - +
369A THR 3.0 17.3 - - - +
370A VAL* 4.5 4.7 - - + -
371A LEU* 4.4 1.3 - - - +
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Residues in contact with HIS 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 4.6 2.9 - - + +
81A GLU* 3.6 43.8 + - + +
82A LEU* 3.6 29.8 - - + +
86A TRP* 4.4 4.9 - + - -
232A THR* 3.6 14.2 - - + +
233A LEU* 3.7 17.2 - - + +
363A ARG* 1.3 68.9 - - - +
365A ASN* 1.3 55.3 + - - +
366A PRO* 3.6 25.9 - - + +
367A THR* 2.5 29.3 + - + +
368A GLY* 2.5 34.7 + - - -
369A THR* 2.9 19.9 + - - -
371A LEU* 4.2 4.7 - - + +
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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