Contacts of the strand formed by residues 414 - 419 (chain A) in PDB entry 3V4P
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 ASP 414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.5 5.6 - - + +
403A GLY* 3.3 23.2 - - - -
405A ILE 2.7 14.2 + - - +
406A ASP* 3.6 5.4 - - - +
407A ALA* 2.6 37.2 + - + +
408A ASP* 3.7 10.9 + - - +
410A ASN* 5.6 0.7 + - - +
412A TYR 4.0 3.3 - - - +
413A VAL* 1.3 78.3 - - - +
415A VAL* 1.3 68.1 + - - +
427A LEU* 4.6 11.0 - - + -
428A LEU 3.6 6.3 - - - +
429A ARG* 3.3 13.4 - - - +
430A THR* 3.1 29.9 + - - +
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Residues in contact with VAL 415 (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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3A VAL* 4.6 7.6 - - + -
25A LEU* 4.1 3.1 - - - -
342A LEU* 3.7 27.1 - - + -
345A ILE* 4.1 11.0 - - + -
354A ALA* 5.5 1.3 - - + -
367A ILE* 4.9 5.8 - - + -
369A ILE* 6.3 1.8 - - + -
401A ILE* 3.9 16.4 - - + -
402A SER 3.5 10.1 - - - +
413A VAL 5.0 0.2 - - - +
414A ASP* 1.3 85.2 - - - +
416A ALA* 1.3 61.7 + - - +
417A VAL* 4.2 10.1 - - + -
427A LEU* 3.4 4.4 - - - +
428A LEU* 2.8 48.5 + - + +
430A THR* 4.1 17.3 - - + -
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Residues in contact with ALA 416 (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* 3.7 10.2 - - + +
25A LEU* 3.7 18.6 - - + +
34A LEU* 3.6 31.9 - - + -
400A SER 4.1 0.2 - - - +
401A ILE* 3.4 5.4 - - - +
402A SER* 2.9 33.5 + - - +
415A VAL* 1.3 73.2 - - - +
417A VAL* 1.3 65.0 + - - +
426A VAL 3.3 9.4 - - - +
427A LEU* 4.6 2.9 - - + -
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Residues in contact with VAL 417 (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* 4.3 4.5 - - - -
367A ILE* 3.6 28.3 - - + -
397A PHE* 3.5 27.4 - - + -
398A GLY* 3.4 33.4 - - - +
400A SER 3.5 4.7 - - - +
401A ILE* 4.2 7.4 - - + -
415A VAL* 4.2 2.9 - - + -
416A ALA* 1.3 80.9 - - - +
418A GLY* 1.3 61.7 + - - +
425A ALA* 3.4 3.6 - - - +
426A VAL* 2.9 36.7 + - + +
428A LEU* 4.1 16.4 - - + -
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Residues in contact with GLY 418 (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 3.4 22.7 - - - -
23A VAL* 3.7 7.8 - - - +
396A MET 3.3 4.2 - - - +
397A PHE* 5.4 0.2 - - - -
398A GLY 2.9 22.9 + - - -
399A GLN* 3.4 7.3 + - - +
400A SER* 2.9 18.0 + - - -
417A VAL* 1.3 74.5 - - - +
419A ALA* 1.3 59.9 + - - -
420A PHE 3.9 0.6 + - - -
424A SER 4.0 4.3 - - - -
425A ALA* 4.4 0.4 - - - -
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Residues in contact with ALA 419 (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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19A PHE 4.0 0.4 - - - -
20A GLY 4.2 0.2 + - - -
394A LEU* 3.9 17.0 - - + -
395A SER 3.2 15.9 - - - +
396A MET 3.6 2.9 - - - -
397A PHE* 3.7 15.7 - - + +
417A VAL 4.2 0.6 + - - -
418A GLY* 1.3 73.7 - - - +
420A PHE* 1.3 58.9 + - - +
421A ARG 3.3 2.7 - - - -
422A SER* 2.9 27.7 + - - +
423A ASP 3.2 2.1 + - - -
424A SER 2.9 29.7 + - - +
425A ALA* 4.5 0.4 - - - +
426A VAL* 6.1 0.7 - - + -
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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