Contacts of the strand formed by residues 355 - 359 (chain A) in PDB entry 2VMX
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 GLY 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A LEU* 4.9 0.7 - - - -
315A VAL 3.0 13.0 - - - -
317A LEU* 4.0 2.7 - - - -
324A GLY* 3.1 18.3 - - - +
340A LYS* 3.4 0.5 - - - -
341A ASN 2.9 34.2 + - - -
343A ILE* 3.7 7.4 - - - +
353A THR* 3.5 1.0 + - - -
354A SER* 1.3 81.2 - - - +
356A ILE* 1.3 62.3 + - - -
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Residues in contact with ILE 356 (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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313A LEU 3.9 0.5 - - - +
314A LEU* 3.5 6.5 - - - -
315A VAL* 3.0 47.1 + - + +
317A LEU* 4.3 4.9 - - + -
324A GLY 3.7 19.7 - - - +
327A ALA* 3.8 12.8 - - + -
328A GLU 4.1 0.2 - - - +
331A LEU* 3.9 24.0 - - + -
338A VAL* 3.8 18.4 - - + -
339A ASN 3.2 11.9 - - - +
340A LYS* 4.2 0.4 - - - -
355A GLY* 1.3 79.7 - - - +
357A ARG* 1.3 60.6 + - - +
358A ILE* 3.8 22.7 + - + +
380A ILE* 5.0 2.7 - - + -
384A LEU* 4.4 16.8 - - + -
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Residues in contact with ARG 357 (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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28A LEU 4.0 4.2 - - - +
29A ILE* 4.0 8.1 - - - +
30A ALA* 3.8 23.5 + - + +
31A SER* 3.7 9.3 + - - +
172A SER* 2.8 40.8 + - - -
173A ALA* 4.1 5.4 - - + -
200A HIS* 3.5 4.0 - - - -
312A LEU* 4.3 10.5 - - + -
313A LEU 3.5 9.9 - - - +
314A LEU* 4.0 5.4 - - + -
338A VAL* 3.8 3.1 - - - +
339A ASN* 2.8 59.9 + - - +
341A ASN* 3.6 28.3 + - + +
356A ILE* 1.3 73.4 - - - +
358A ILE* 1.3 65.9 + - - +
502A ALO 2.9 43.0 + - - +
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Residues in contact with ILE 358 (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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28A LEU* 3.4 18.8 - - + -
30A ALA* 4.0 4.0 - - - -
292A LEU* 3.6 29.6 - - + -
296A LEU* 4.5 3.8 - - + -
312A LEU* 3.3 4.3 - - - +
313A LEU* 2.8 59.1 + - + +
315A VAL* 4.2 7.4 - - + -
338A VAL* 3.8 18.2 - - + -
356A ILE* 3.8 25.6 - - + -
357A ARG* 1.3 80.2 - - - +
359A GLY* 1.3 63.7 + - - +
360A THR* 5.5 0.2 - - + -
380A ILE* 4.1 22.4 - - + -
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Residues in contact with GLY 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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27A GLU 4.4 2.6 - - - +
28A LEU* 2.9 36.1 + - - +
29A ILE 4.8 0.7 - - - +
30A ALA* 3.8 22.2 - - - +
311A HIS* 3.1 12.3 - - - -
358A ILE* 1.3 76.3 - - - +
360A THR* 1.3 64.1 + - - -
361A ALA 3.6 2.2 - - - -
362A ALA* 5.1 0.9 + - - +
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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