Contacts of the strand formed by residues 407 - 413 (chain A) in PDB entry 3V4O
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 TYR 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU 3.7 2.1 + - - -
340A ALA* 3.5 31.6 - - + -
342A ASP 2.9 12.5 + - - +
343A LYS* 3.6 15.9 - - + -
344A VAL 2.9 28.6 + - - +
378A PHE* 4.3 8.9 - + + -
405A GLY 4.0 4.5 - - - -
406A VAL* 1.3 76.5 - - - +
408A GLY* 1.3 61.0 + - - +
455A GLY* 4.5 2.2 - - - -
456A LEU* 3.6 35.4 - - + -
558A ARG* 2.9 44.7 + - + -
559A ALA 3.4 25.8 - - - -
560A LEU* 5.0 2.5 - - - -
562A ASP* 2.5 29.9 + - + +
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Residues in contact with GLY 408 (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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344A VAL 3.5 5.2 - - - -
378A PHE* 5.4 0.2 - - - -
398A PHE* 4.2 1.6 - - - -
402A LEU* 3.9 19.4 - - - +
406A VAL 3.6 2.6 + - - -
407A TYR* 1.3 74.7 - - - +
409A LEU* 1.3 58.9 + - - +
449A MET* 3.9 15.2 - - - +
454A THR* 4.8 0.8 - - - +
456A LEU* 2.9 17.5 + - - +
457A ASN* 3.5 1.7 - - - -
458A VAL* 3.0 25.9 + - - +
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A VAL 2.9 8.2 + - - +
345A ALA* 3.1 15.3 - - + +
346A LEU 2.8 26.3 + - - -
347A LEU* 4.3 1.1 - - + -
369A LEU* 4.7 0.4 - - + -
373A LEU* 4.1 32.5 - - + -
378A PHE* 4.2 8.3 - - + -
398A PHE* 3.6 8.1 - - - -
408A GLY* 1.3 74.4 - - - +
410A LEU* 1.3 74.6 + - - +
411A TYR* 4.0 12.3 - - + +
458A VAL* 3.3 32.8 - - + +
460A LEU* 4.3 14.8 - - + -
560A LEU* 4.3 26.7 - - + -
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Residues in contact with LEU 410 (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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346A LEU* 3.4 41.3 - - + +
348A ILE* 4.9 6.5 - - + -
395A VAL* 5.3 4.5 - - + -
398A PHE* 4.8 11.4 - - + -
409A LEU* 1.3 77.9 - - - +
411A TYR* 1.3 66.6 + - - +
412A TYR* 4.9 0.9 - - + -
425A MET* 4.1 32.1 - - + -
442A VAL* 5.1 2.2 - - + -
445A ILE* 4.6 11.0 - - + -
449A MET* 5.7 0.6 - - - +
458A VAL 2.9 6.9 + - - +
459A PHE* 3.5 31.6 - - + -
460A LEU 2.9 25.6 + - - +
461A LEU* 4.4 10.5 - - + -
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Residues in contact with TYR 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU 2.9 8.0 + - - +
347A LEU* 3.4 19.2 - - + -
348A ILE* 2.9 26.9 + - - +
365A ASP* 3.3 21.1 - - + +
366A VAL* 4.0 20.9 - - + -
369A LEU* 3.4 30.5 - - + -
409A LEU* 4.0 4.2 - - + +
410A LEU* 1.3 77.4 - - - +
412A TYR* 1.3 60.5 + - - +
413A ALA* 3.5 25.1 - - + +
460A LEU* 3.3 28.3 - - + -
462A ASP* 2.6 37.0 + - + -
511A PHE* 4.1 8.1 - + - -
512A MET* 3.5 23.0 - - + +
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Residues in contact with TYR 412 (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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348A ILE* 3.4 19.1 - - + -
350A ASN* 3.4 20.5 + - - -
353A TYR* 2.9 20.6 + - - -
391A MET* 4.1 10.5 - - + -
410A LEU* 4.8 2.7 - - + +
411A TYR* 1.3 79.1 - - - +
413A ALA* 1.3 64.1 + - - +
414A GLY* 3.6 18.3 - - - -
415A HIS 2.8 29.3 + - - -
425A MET* 3.5 44.4 - - + -
426A VAL 3.0 8.0 + - - -
460A LEU 3.1 6.9 + - - -
461A LEU* 4.4 9.2 - - + -
462A ASP* 2.8 34.5 + - - +
463A MET* 3.7 17.0 - - + -
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Residues in contact with ALA 413 (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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348A ILE 2.9 9.7 + - - +
349A GLY* 3.3 2.3 - - - -
350A ASN 2.8 25.8 + - - +
362A PRO* 3.8 22.8 - - + +
365A ASP* 4.8 0.4 - - + -
411A TYR* 3.5 30.4 - - + +
412A TYR* 1.3 76.3 - - - +
414A GLY* 1.3 58.5 + - - +
462A ASP 3.4 5.2 - - - -
5B ARG* 3.7 14.4 - - - +
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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