Contacts of the strand formed by residues 397 - 405 (chain A) in PDB entry 3V4V
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 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A PRO* 3.3 6.8 - - - +
364A GLN 3.1 17.6 + - - +
365A GLY* 3.1 6.5 - - - +
366A ALA* 3.0 33.2 + - - -
367A ILE* 3.7 22.7 - - + -
385A ILE* 3.8 23.8 - - + -
386A GLU 4.5 0.7 - - - -
387A GLY* 3.8 21.1 - - - -
390A ILE* 4.5 8.3 - - + -
394A LEU* 4.1 16.8 - - + -
395A SER 3.2 2.0 - - - -
396A MET* 1.3 74.7 - - - +
398A GLY* 1.3 59.0 + - - +
417A VAL* 3.5 30.7 - - + -
418A GLY 5.2 0.4 - - - -
419A ALA* 3.6 17.9 - - + -
426A VAL* 4.2 20.9 - - + -
428A LEU* 4.7 7.0 - - + -
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Residues in contact with GLY 398 (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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338A SER* 3.0 18.2 + - - -
356A GLY* 3.4 10.0 - - - -
358A PRO* 4.2 6.5 - - - +
366A ALA 4.4 2.5 - - - -
367A ILE* 3.5 25.6 - - - -
397A PHE* 1.3 76.4 - - - +
399A GLN* 1.3 65.5 + - - +
400A SER* 3.2 3.7 + - - -
401A ILE* 4.3 1.4 - - - +
417A VAL* 3.7 7.7 - - - +
418A GLY 3.0 9.1 + - - -
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Residues in contact with GLN 399 (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 GLY 4.8 2.0 - - - +
21A TYR* 3.8 43.7 + - + +
337A GLU* 3.8 29.1 + - - +
338A SER* 3.6 14.3 - - - -
358A PRO* 3.9 13.8 - - + +
359A GLN* 5.9 0.7 + - - -
396A MET* 3.4 9.5 + - - +
397A PHE 3.6 0.2 - - - -
398A GLY* 1.3 78.2 - - - +
400A SER* 1.3 58.9 + - - +
418A GLY 3.5 3.9 + - - +
420A PHE* 3.4 45.0 - - + -
280B LYS* 5.7 2.2 - - - +
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Residues in contact with SER 400 (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 GLY 2.9 20.4 + - - -
21A TYR 3.4 17.0 - - - -
22A SER* 3.4 18.2 - - - -
23A VAL* 3.5 12.6 - - - +
338A SER* 4.5 2.7 - - - -
398A GLY 4.2 0.2 - - - -
399A GLN* 1.3 81.5 - - - +
401A ILE* 1.3 68.3 + - - +
417A VAL* 3.4 3.5 - - - +
418A GLY* 2.9 27.7 + - - -
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Residues in contact with ILE 401 (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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23A VAL* 4.4 5.2 - - - +
338A SER* 4.1 13.2 + - - +
340A VAL* 3.3 35.4 - - + +
354A ALA* 3.8 24.5 - - + +
355A ILE 4.0 0.4 - - - -
356A GLY* 3.9 20.4 - - - +
367A ILE* 3.6 31.4 - - + -
398A GLY 4.3 3.6 - - - +
400A SER* 1.3 81.4 - - - +
402A SER* 1.3 66.1 + - - +
415A VAL* 3.7 22.7 - - + -
416A ALA 3.2 12.8 - - - +
417A VAL* 4.2 4.0 - - + -
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Residues in contact with SER 402 (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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23A VAL* 3.3 25.5 - - - +
24A VAL* 3.6 16.6 - - - +
25A LEU* 3.4 20.3 + - - +
340A VAL* 3.7 9.4 - - - +
342A LEU* 4.8 1.3 - - - -
401A ILE* 1.3 77.4 - - - +
403A GLY* 1.3 65.6 + - - +
415A VAL* 3.6 3.2 - - - +
416A ALA 2.8 33.0 + - - -
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Residues in contact with GLY 403 (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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25A LEU* 3.7 5.6 - - - +
340A VAL* 4.0 9.5 - - - +
342A LEU* 4.3 11.9 - - - +
402A SER* 1.3 83.1 + - - +
404A GLN* 1.3 66.0 + - - +
405A ILE* 3.0 21.9 + - - +
414A ASP 3.2 17.3 - - - -
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Residues in contact with GLN 404 (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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102A PRO* 5.4 12.7 - - - +
172A PHE* 6.0 2.9 - - - -
340A VAL* 5.4 2.4 - - + +
341A ASN* 3.5 30.5 - - - +
342A LEU* 3.4 20.9 + - - +
343A GLY* 4.1 5.2 - - - +
403A GLY* 1.3 72.8 - - - +
405A ILE* 1.3 67.9 + - + +
413A VAL* 3.1 32.6 - - - +
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Residues in contact with ILE 405 (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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25A LEU* 3.4 45.1 - - + +
26A HIS 4.5 3.1 - - - +
27A SER* 3.6 40.2 - - - +
32A ARG* 4.6 5.2 - - - -
100A ARG* 3.7 22.9 - - - +
403A GLY 3.0 5.6 + - - +
404A GLN* 1.3 90.8 - - + +
406A ASP* 1.3 72.0 - - - +
407A ALA* 3.5 7.0 + - + +
413A VAL* 3.8 3.3 - - - +
414A ASP* 3.0 25.0 + - - +
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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
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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