Contacts of the strand formed by residues 444 - 450 (chain A) in PDB entry 1M2V
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 THR 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A ASN* 3.6 27.6 - - - +
404A MET 3.1 12.3 - - - +
405A ALA* 3.9 12.0 - - + +
407A LYS* 5.4 2.4 + - - -
424A VAL* 3.0 36.4 + - + -
427A THR* 3.9 21.0 - - + +
429A ALA* 5.4 1.4 - - - +
442A THR* 2.9 14.9 + - - +
443A SER* 1.3 85.5 + - - +
445A TRP* 1.3 71.0 + - - +
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Residues in contact with TRP 445 (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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403A ASN* 3.5 5.4 + - - -
404A MET* 2.9 40.7 + - + +
406A VAL* 4.1 17.5 - - + -
414A VAL* 3.5 19.5 - - + -
416A GLY 3.7 4.7 - - - -
417A LEU* 3.4 56.1 - - + +
421A ALA* 4.0 9.4 - - + -
422A SER 3.2 10.1 - - - +
423A ALA* 3.8 18.6 - - - -
424A VAL* 3.6 6.2 - - - +
439A ILE* 3.0 31.2 + - + +
442A THR* 3.2 37.1 - - + +
443A SER* 3.3 19.3 - - - -
444A THR* 1.3 74.6 - - - +
446A LYS* 1.3 61.5 + - - +
447A MET* 4.2 4.7 - - + -
458A ILE* 4.8 5.8 - - + -
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Residues in contact with LYS 446 (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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337A ALA* 3.1 30.0 + - - +
338A ALA* 4.4 12.9 - - - +
340A GLY* 5.6 1.8 - - - +
364A SER 4.3 2.1 - - - +
401A ASN* 6.0 0.9 - - - +
402A GLY 3.3 11.7 - - - +
403A ASN* 4.5 6.1 - - - +
421A ALA* 3.2 5.2 - - - -
422A SER* 2.8 52.0 + - - +
423A ALA 3.7 17.8 + - - -
424A VAL* 3.8 15.3 - - + +
445A TRP* 1.3 76.9 - - - +
447A MET* 1.3 66.6 + - - +
448A ALA 4.3 1.1 - - - +
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Residues in contact with MET 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A SER 5.2 0.9 - - - -
366A GLY 4.9 0.9 - - - +
401A ASN* 4.7 0.4 - - - -
402A GLY* 2.7 48.4 + - - +
404A MET* 3.9 31.4 - - + -
417A LEU* 4.6 4.3 - - + -
420A HIS 3.5 22.0 - - - +
421A ALA* 3.8 8.5 - - + +
445A TRP* 4.2 3.8 - - + +
446A LYS* 1.3 89.5 - - - +
448A ALA* 1.3 63.1 + - - +
449A SER* 3.2 20.6 + - - +
450A LEU* 4.2 10.8 - - + -
456A TYR* 3.5 44.4 - - + +
491A THR* 5.7 0.4 - - + -
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Residues in contact with ALA 448 (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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281A PRO* 5.9 0.7 - - - +
337A ALA* 5.8 0.9 - - - -
340A GLY* 4.0 11.3 - - - +
341A HIS 3.4 32.3 - - - +
342A THR* 3.4 17.3 + - - +
364A SER 5.2 0.2 + - - -
365A THR* 3.8 17.0 - - + +
366A GLY 4.1 3.4 - - - +
400A PHE* 3.2 9.7 - - - +
401A ASN* 2.9 26.1 + - - +
446A LYS* 4.3 0.8 - - - +
447A MET* 1.3 70.5 - - - +
449A SER* 1.3 61.2 + - - +
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Residues in contact with SER 449 (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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283A ARG* 3.3 24.6 + - - -
342A THR* 2.9 25.8 + - - -
366A GLY* 3.1 40.4 - - - +
399A ALA 3.5 4.8 + - - -
400A PHE* 3.8 11.6 - - - -
447A MET* 3.4 9.8 - - - +
448A ALA* 1.3 81.3 + - - +
450A LEU* 1.3 65.8 + - - +
454A HIS* 4.4 1.6 + - - -
456A TYR* 4.5 0.9 + - - -
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Residues in contact with LEU 450 (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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39A PRO* 4.9 6.1 - - + -
40A LEU* 3.7 21.8 - - + -
283A ARG* 5.7 0.2 + - - -
398A MET* 3.7 2.4 - - - +
399A ALA* 2.8 66.2 + - + +
400A PHE* 3.8 9.9 - - - +
402A GLY* 4.3 17.0 - - - -
447A MET* 4.2 13.9 - - + -
449A SER* 1.3 77.7 - - - +
451A SER* 1.3 66.7 + - - +
454A HIS* 3.8 12.8 - - + -
456A TYR* 3.5 20.6 - - + +
491A THR* 4.3 16.4 - - + -
493A TYR* 4.7 3.1 - - + -
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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