Contacts of the strand formed by residues 500 - 512 (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 ASN 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ILE* 3.6 1.6 - - - -
114A THR* 2.9 38.6 + - + +
115A ASN* 2.7 39.4 + - - +
117A PRO* 3.1 30.5 - - - +
401A ASN* 5.8 1.0 + - - -
492A THR* 5.6 2.9 - - - +
493A TYR 3.5 5.6 - - - +
494A GLN* 3.6 21.1 + - - +
499A THR* 1.3 74.9 - - - +
501A ARG* 1.3 62.3 + - - +
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Residues in contact with ARG 501 (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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48A VAL* 4.5 14.8 - - - +
111A GLU* 3.3 40.2 + - - +
112A TYR 3.0 9.0 - - - +
113A ILE* 4.1 27.3 - - - +
114A THR* 3.7 0.8 - - - +
492A THR* 3.3 2.1 + - - -
493A TYR* 2.9 38.8 + - + +
495A HIS* 3.5 37.0 + - + -
497A SER* 3.2 24.0 + - - -
499A THR* 3.5 13.8 + - - +
500A ASN* 1.3 79.9 - - - +
502A ILE* 1.3 71.3 + - - +
503A ARG 4.2 0.7 - - - -
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Residues in contact with ILE 502 (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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53A PRO* 4.2 16.4 - - + -
64A ILE* 4.3 7.2 - - + -
111A GLU* 3.3 4.4 - - - -
112A TYR* 2.8 49.5 + - + +
114A THR* 3.8 27.1 - - + +
490A ILE* 3.5 30.5 - - + -
491A THR 3.7 5.4 - - - +
492A THR* 4.0 13.7 - - - +
501A ARG* 1.3 81.0 - - - +
503A ARG* 1.3 62.0 + - - +
504A VAL* 3.9 13.0 - - + -
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Residues in contact with ARG 503 (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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37A TYR* 4.3 10.0 + - - +
39A PRO 3.1 31.3 + - - +
40A LEU* 3.7 18.8 + - + +
41A LYS 2.7 29.5 + - - -
42A GLU* 5.0 0.2 - - - +
43A TYR* 4.1 3.2 - - - -
46A LEU* 3.5 27.3 - - - +
109A THR* 4.3 11.1 - - + +
110A ILE 3.4 15.9 - - - -
111A GLU* 2.5 47.6 + - - +
489A PHE 3.3 2.6 - - - +
490A ILE* 3.5 2.3 - - - -
491A THR* 2.9 46.3 + - - +
493A TYR* 3.7 6.9 + - - -
501A ARG 4.2 0.2 - - - -
502A ILE* 1.3 72.0 - - - +
504A VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 504 (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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64A ILE* 3.8 31.0 - - + -
65A LEU 5.4 2.0 - - - +
66A ASN* 5.6 0.9 - - + -
108A THR 4.2 1.6 - - - +
109A THR* 3.0 7.6 - - - +
110A ILE* 2.8 45.0 + - + +
112A TYR* 4.0 13.2 - - + -
488A GLN* 3.4 36.1 - - + +
489A PHE 3.3 1.8 - - - -
490A ILE* 4.4 5.4 - - + -
502A ILE* 3.9 10.5 - - + -
503A ARG* 1.3 81.0 - - - +
505A THR* 1.3 66.7 + - - +
506A THR* 3.8 5.8 - - - +
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Residues in contact with THR 505 (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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10A ASN* 3.8 20.5 + - + -
12A VAL* 4.0 10.5 - - + -
37A TYR* 2.6 32.2 + - - -
108A THR 3.3 4.5 - - - -
109A THR* 2.7 26.1 + - - +
488A GLN* 3.2 4.0 - - - +
489A PHE* 2.7 49.2 + - + -
504A VAL* 1.3 74.1 + - - +
506A THR* 1.3 65.5 + - - +
507A VAL* 4.2 8.1 - - + -
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Residues in contact with THR 506 (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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10A ASN* 4.7 0.2 + - - -
66A ASN* 3.5 37.9 - - - +
67A PRO* 5.3 0.2 - - - -
68A TYR* 3.7 15.9 - - + -
81A PRO* 6.0 1.1 - - + -
82A ILE* 5.3 4.9 - - + -
108A THR* 2.9 31.6 + - - -
486A TYR* 5.3 3.6 - - + -
487A THR 3.3 15.7 - - - +
488A GLN* 3.1 30.3 + - + -
504A VAL* 3.8 4.2 - - - +
505A THR* 1.3 75.6 - - - +
507A VAL* 1.3 71.4 + - - +
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Residues in contact with VAL 507 (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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6A ASN* 4.4 9.4 - - - +
10A ASN* 4.3 14.4 - - - +
12A VAL* 4.7 7.4 - - + -
14A PHE* 3.9 29.8 - - + -
68A TYR* 4.2 7.6 - - - -
485A ALA 3.9 0.2 - - - +
486A TYR* 3.4 6.9 - - - +
487A THR* 2.8 56.3 + - + +
489A PHE* 4.4 5.2 - - + -
505A THR* 4.2 15.9 - - + -
506A THR* 1.3 82.3 - - - +
508A ALA* 1.3 62.0 + - - +
509A ASN* 3.9 7.4 - - - +
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Residues in contact with ALA 508 (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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68A TYR* 3.9 25.5 + - + -
484A LEU* 4.7 12.1 - - + -
485A ALA 3.3 4.7 - - - -
486A TYR* 3.6 28.3 - - + -
507A VAL* 1.3 75.8 - - - +
509A ASN* 1.3 69.7 + - - +
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Residues in contact with ASN 509 (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* 3.9 24.1 - - - -
17A ASN* 3.4 25.8 - - - +
19A PHE* 3.4 48.3 - - + -
484A LEU* 3.9 3.8 - - - -
485A ALA* 2.7 43.4 + - - +
487A THR* 5.2 1.8 + - - -
507A VAL* 3.9 13.3 - - - +
508A ALA* 1.3 82.4 + - - +
510A GLN* 1.3 61.9 + - - +
511A LEU* 3.6 0.4 - - - +
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Residues in contact with GLN 510 (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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17A ASN 4.8 3.4 + - - -
18A VAL* 3.3 19.7 - - + +
19A PHE* 3.0 23.2 + - - -
482A PRO* 4.5 21.2 - - - +
483A HIS 3.7 8.7 - - - +
484A LEU* 3.4 19.6 - - + +
509A ASN* 1.3 72.9 - - - +
511A LEU* 1.3 69.7 + - - +
512A LEU* 4.1 27.3 - - + +
518A ALA* 5.5 1.4 - - - +
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Residues in contact with LEU 511 (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* 3.3 14.6 - - + +
20A PRO 3.5 19.5 - - - +
21A SER* 3.9 12.0 - - - -
411A ASP* 4.3 9.9 - - - +
462A ILE* 4.2 11.7 - - + -
464A ASN* 3.8 25.1 - - - +
483A HIS* 2.8 44.1 + - + +
484A LEU 3.9 5.2 - - - -
485A ALA* 3.2 38.6 - - + +
509A ASN 3.6 6.7 - - - +
510A GLN* 1.3 73.1 - - - +
512A LEU* 1.3 68.3 + - - +
513A PRO* 4.7 0.5 - - - +
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Residues in contact with LEU 512 (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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18A VAL* 3.8 12.8 - - + -
19A PHE 3.2 6.5 + - - -
20A PRO* 3.8 0.3 - - - +
21A SER* 3.0 24.1 + - - -
483A HIS 6.4 0.2 - - - +
510A GLN* 4.1 24.8 + - + +
511A LEU* 1.3 83.0 - - - +
513A PRO* 1.3 80.3 - - + +
516A THR* 3.5 24.9 - - + +
518A ALA* 3.4 32.8 - - + -
519A ILE* 3.7 16.3 - - + +
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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