Contacts of the strand formed by residues 407 - 412 (chain A) in PDB entry 4MJV
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 SER 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A LYS* 3.2 26.4 + - - +
351A GLY* 3.3 25.1 - - - -
352A PHE* 3.4 23.7 - - - -
363A GLY 5.6 0.5 - - - -
374A PHE* 3.6 23.2 - - - -
405A GLY 4.2 1.2 + - - -
406A TYR* 1.3 77.5 - - - +
408A GLY* 1.3 58.0 + - - +
423A TRP* 3.3 19.5 - - - -
424A VAL* 4.6 2.0 - - - -
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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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228A SER* 3.8 3.6 - - - -
279A SER* 3.7 12.6 - - - -
350A LYS* 4.2 0.4 - - - -
352A PHE* 4.0 7.8 - - - -
407A SER* 1.3 76.8 - - - +
409A SER* 1.3 60.1 + - - -
422A PHE* 3.2 22.3 - - - +
423A TRP* 3.2 36.4 + - - -
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Residues in contact with SER 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL 4.5 0.5 - - - +
228A SER* 3.5 13.4 + - - -
229A SER* 3.9 6.6 - - - -
279A SER* 3.1 26.1 + - - -
280A CYS 2.8 29.2 + - - +
281A TYR* 4.0 3.0 - - - -
352A PHE* 4.3 8.1 - - - -
353A GLY 5.2 0.7 - - - -
354A PHE* 3.5 28.0 - - - -
408A GLY* 1.3 74.6 - - - -
410A PHE* 1.3 66.8 + - - +
421A CYS 3.5 5.8 - - - -
422A PHE* 4.6 0.2 - - - +
423A TRP* 4.7 0.6 + - - -
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Residues in contact with PHE 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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100A PHE* 4.7 3.1 - + - -
122A VAL* 3.3 53.6 - - + +
123A SER* 4.5 2.0 - - - -
124A CYS* 3.7 26.7 - - - +
129A CYS* 4.7 0.9 - - - -
229A SER* 4.1 9.4 - - - +
280A CYS 4.6 5.2 - - - -
281A TYR* 5.0 2.2 - - - +
354A PHE* 3.9 4.2 - - - -
409A SER* 1.3 78.9 - - - +
411A THR* 1.3 69.2 + - - +
412A LEU* 4.3 6.1 - - + -
421A CYS* 3.1 63.0 + - + +
422A PHE 3.9 9.2 - - - -
423A TRP* 4.2 7.2 - + - -
445A VAL* 3.6 25.1 - - + -
447A CYS* 4.3 1.1 - - - -
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Residues in contact with THR 411 (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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87A ASN* 4.7 5.5 + - - -
91A ILE* 3.6 30.5 - - + -
124A CYS* 4.1 5.4 + - - +
281A TYR* 4.3 3.6 - - + -
282A PRO* 3.4 32.3 - - + +
410A PHE* 1.3 90.5 - - - +
412A LEU* 1.3 81.7 + - - +
418A LEU* 3.8 13.7 - - + -
419A VAL 3.3 11.7 - - - +
420A PRO* 4.6 1.1 - - + -
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Residues in contact with LEU 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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100A PHE* 4.2 14.4 - - + -
129A CYS* 4.2 24.5 - - - -
410A PHE* 4.3 4.3 - - + -
411A THR* 1.3 70.8 - - - +
412A PRO* 1.3 73.4 + - + +
413A SER* 4.1 24.2 + - - +
417A CYS 4.8 0.3 - - - +
418A LEU* 4.0 10.2 - - - +
419A VAL* 2.9 48.8 + - + -
421A CYS* 3.7 23.5 - - - -
447A CYS* 4.7 4.7 - - + -
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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