Contacts of the strand formed by residues 388 - 393 (chain A) in PDB entry 3V4R
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 ASN 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.9 27.2 + - + +
31A GLY* 5.0 1.9 - - - -
32A LYS 2.9 25.3 - - - +
33A LYS* 3.9 3.1 - - - +
58A LYS* 3.5 22.6 - - - +
333A PHE 3.7 6.7 + - - +
334A MET* 3.4 16.2 - - + +
335A ILE* 3.1 26.0 + - - +
387A HIS* 1.4 102.7 + - - +
389A ILE* 1.4 60.4 + - - +
390A VAL* 5.6 0.4 - - - -
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Residues in contact with ILE 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 2.8 34.1 + - + +
34A HIS* 3.4 33.4 - - + +
35A GLN* 3.0 17.9 + - - +
335A ILE* 3.6 31.4 - - + -
337A VAL* 3.8 11.4 - - + -
382A PHE* 4.7 5.6 - - + -
386A MET* 4.2 33.7 - - + -
388A ASN* 1.4 72.7 - - - +
390A VAL* 1.3 69.7 + - - +
391A TYR* 3.5 30.3 - - + +
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.2 21.8 - - + -
28A ILE* 4.5 9.0 - - + -
35A GLN* 3.3 26.7 - - + +
37A LEU* 4.5 7.0 - - + +
49A VAL* 5.8 2.2 - - + -
52A LEU* 4.3 21.5 - - + -
334A MET* 4.7 4.5 - - + -
335A ILE 3.0 14.4 + - - +
336A VAL* 3.3 13.3 - - + +
337A VAL 2.9 24.7 + - - -
389A ILE* 1.3 79.2 - - - +
391A TYR* 1.3 71.0 + - - +
392A VAL* 3.8 12.6 + - + -
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Residues in contact with TYR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A HIS* 2.8 42.3 + - + -
35A GLN 2.9 27.1 + - - -
36A THR* 3.2 20.4 - - + +
37A LEU 2.7 32.7 + - - +
337A VAL* 4.0 17.5 - - + -
340A SER* 3.7 7.9 - - - +
344A ILE* 3.9 21.5 - - + -
386A MET* 4.1 1.6 - - - -
389A ILE* 3.5 33.2 - - + +
390A VAL* 1.3 72.2 - - - +
392A VAL* 1.3 56.4 + - - +
399A TYR* 3.1 26.7 + + - -
400A GLU* 3.5 31.4 - - + -
403A HIS* 5.0 0.7 - - + -
404A THR* 4.5 0.9 - - - -
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.6 26.9 - - + +
39A GLY 5.3 0.2 - - - +
45A LYS* 4.2 29.2 - - + -
49A VAL* 4.2 14.6 - - + -
336A VAL* 3.8 28.9 - - + -
337A VAL 2.9 12.8 + - - +
338A ASP* 4.4 10.5 - - - +
339A GLU* 2.9 27.0 + - - -
340A SER* 3.1 7.3 + - - -
390A VAL* 4.1 9.6 - - + +
391A TYR* 1.3 76.9 - - - +
393A SER* 1.3 62.3 + - - +
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Residues in contact with SER 393 (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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36A THR* 5.4 0.4 - - - +
37A LEU 3.2 9.4 + - - +
38A LEU* 3.4 5.2 - - - -
39A GLY 3.3 19.6 + - - -
45A LYS* 4.9 1.8 - - - +
339A GLU* 4.3 8.1 - - - -
340A SER* 3.2 19.7 - - - -
341A HIS* 2.7 30.0 + - - -
391A TYR 4.2 0.6 - - - -
392A VAL* 1.3 77.6 - - - +
394A ALA* 1.3 64.6 + - - +
395A THR 3.1 11.3 + - - -
396A PRO* 3.8 17.0 - - - +
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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
------------------------------------------------------------
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