Contacts of the strand formed by residues 484 - 494 (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 LEU 484 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 6.2 1.1 - - + -
409A SER* 4.6 1.4 + - - -
411A ASP* 3.8 12.6 - - - +
482A PRO* 3.9 12.3 + - + +
483A HIS* 1.3 85.9 + - - +
485A ALA* 1.3 61.5 + - - +
486A TYR* 3.6 41.4 - - + +
508A ALA* 4.7 8.3 - - + -
509A ASN* 3.5 4.7 - - - +
510A GLN* 3.4 39.5 - - + +
511A LEU* 3.9 3.1 - - - -
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 4.2 15.4 - - + -
409A SER* 3.6 4.0 - - - -
411A ASP* 4.1 12.1 - - - +
412A LEU* 4.2 14.6 - - + -
484A LEU* 1.3 73.6 - - - +
486A TYR* 1.3 62.2 + - - +
487A THR 4.3 0.2 + - - -
507A VAL 3.9 0.2 - - - +
508A ALA* 3.3 4.2 - - - -
509A ASN* 2.7 37.6 + - - +
511A LEU* 3.2 25.1 - - + -
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Residues in contact with TYR 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 3.6 32.3 + + + -
81A PRO* 3.6 36.1 - - + -
82A ILE* 3.6 16.4 - - + +
84A ASN* 6.3 0.2 - - - -
408A THR* 3.2 5.9 - - - -
409A SER* 2.5 48.6 + - - +
412A LEU* 4.3 1.1 - - - +
484A LEU* 3.6 35.6 - - + +
485A ALA* 1.3 74.7 - - - +
487A THR* 1.3 63.9 + - - +
506A THR* 5.3 3.1 - - + -
507A VAL 3.4 5.4 - - - +
508A ALA* 3.6 29.2 - - + -
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Residues in contact with THR 487 (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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14A PHE* 4.8 4.7 - - + -
19A PHE* 5.1 1.7 - - - -
82A ILE* 4.4 0.4 - - - -
406A VAL* 4.1 6.1 - - + -
407A LYS 3.3 9.9 - - - +
408A THR* 3.9 1.1 - - + +
412A LEU* 3.3 26.7 - - - +
460A PHE* 3.8 21.5 - - + -
485A ALA 5.3 0.3 + - - -
486A TYR* 1.3 73.5 - - - +
488A GLN* 1.3 63.9 + - - +
489A PHE* 3.7 29.8 - - + -
505A THR 3.9 0.2 - - - +
506A THR* 3.3 5.6 - - - +
507A VAL* 2.8 48.5 + - + +
509A ASN* 5.2 1.2 + - - +
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Residues in contact with GLN 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER* 2.6 26.9 + - - -
64A ILE 2.7 37.1 + - - -
65A LEU 4.4 0.2 + - - -
66A ASN* 3.6 6.0 - - - +
82A ILE* 4.3 6.1 - - + -
405A ALA 3.4 4.3 - - - +
406A VAL* 3.6 0.9 - - - -
407A LYS* 2.8 44.3 + - + +
487A THR* 1.3 77.1 - - - +
489A PHE* 1.3 61.9 + - - +
490A ILE* 3.5 13.4 + - + +
504A VAL* 3.4 22.3 - - + +
505A THR 3.2 13.2 - - - +
506A THR* 3.1 24.0 + - + +
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Residues in contact with PHE 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 4.3 14.1 - - + -
14A PHE* 4.9 1.3 - + - -
35A CYS* 3.6 24.2 - - - -
37A TYR* 3.2 40.9 + + + +
404A MET* 4.8 3.6 - - + -
405A ALA 3.7 3.6 - - - -
406A VAL* 3.7 23.6 - - + -
458A ILE* 3.8 27.4 - - + -
460A PHE* 4.3 3.1 - + - -
487A THR* 3.7 24.0 - - + -
488A GLN* 1.3 73.8 - - - +
490A ILE* 1.3 62.2 + - - +
491A THR* 3.8 1.8 - - - +
503A ARG 3.3 2.3 - - - +
504A VAL* 3.3 6.9 - - - +
505A THR* 2.7 49.9 + - + +
507A VAL* 4.4 12.6 - - + -
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Residues in contact with ILE 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS 3.8 22.0 - - - +
64A ILE* 4.1 13.7 - - + -
403A ASN* 3.3 4.9 - - - +
404A MET* 5.3 0.2 - - - +
405A ALA* 2.9 43.5 + - + +
407A LYS* 4.0 20.2 - - + -
488A GLN* 3.5 31.0 - - + +
489A PHE* 1.3 77.4 - - - +
491A THR* 1.3 57.4 + - - +
492A THR* 3.7 7.3 + - + +
502A ILE* 3.5 29.6 - - + -
503A ARG 3.5 2.0 - - - -
504A VAL* 4.4 5.2 - - + -
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Residues in contact with THR 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 4.0 7.4 + - - -
39A PRO* 3.3 23.5 - - + +
40A LEU* 4.8 1.1 - - + -
403A ASN 3.3 13.5 - - - +
404A MET* 3.0 31.5 - - + +
447A MET* 5.7 1.1 - - + -
450A LEU* 4.3 20.4 - - + -
490A ILE* 1.3 72.9 - - - +
492A THR* 1.3 65.8 + - - +
493A TYR* 3.5 13.2 - - + -
502A ILE* 4.4 0.7 - - - -
503A ARG* 2.9 39.5 + - - -
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Residues in contact with THR 492 (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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114A THR* 5.1 3.3 - - - +
401A ASN 3.7 1.1 - - - +
402A GLY* 3.5 0.2 - - - -
403A ASN* 2.7 61.0 + - + +
490A ILE* 3.7 7.4 + - + +
491A THR* 1.3 73.4 - - - +
493A TYR* 1.3 62.2 + - - +
500A ASN* 5.6 2.3 - - - +
501A ARG 3.3 12.2 + - - -
502A ILE* 4.0 21.0 - - - +
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Residues in contact with TYR 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.4 28.8 - - + +
111A GLU* 2.6 37.0 + - - -
399A ALA* 3.5 30.1 - - + -
400A PHE 3.7 7.4 - - - +
401A ASN* 3.4 9.2 - - - -
402A GLY* 3.7 11.0 - - - -
450A LEU* 4.7 5.6 - - + -
491A THR* 3.5 19.1 - - + -
492A THR* 1.3 77.7 + - - +
494A GLN* 1.3 63.2 + - - +
495A HIS* 3.9 30.4 - + + -
500A ASN* 3.5 7.6 - - - +
501A ARG* 2.9 45.6 + - + -
503A ARG* 3.7 6.6 + - + -
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Residues in contact with GLN 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO* 4.1 23.9 - - + +
119A THR 5.5 1.0 + - - +
120A VAL 4.7 11.7 + - - -
122A PRO* 5.3 7.9 - - - +
281A PRO* 3.4 37.0 - - - +
399A ALA* 3.8 2.1 - - - -
400A PHE* 2.9 50.9 + - + +
401A ASN* 4.0 10.7 + - + +
493A TYR* 1.3 74.5 - - - +
495A HIS* 1.3 70.5 + - - +
496A SER 3.9 0.2 + - - -
498A GLY* 5.4 3.5 - - - -
499A THR 3.8 2.5 - - - +
500A ASN* 3.6 17.7 - - - +
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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