Contacts of the strand formed by residues 437 - 448 (chain D) in PDB entry 2VM8
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 MET 437 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284D GLY* 3.2 30.1 - - - +
285D THR* 5.3 1.1 - - - -
364D VAL* 4.5 13.2 - - + -
367D ASP* 5.3 5.2 - - - +
368D LYS* 5.7 4.9 - - + -
418D LYS 3.5 0.7 - - - +
420D ILE* 2.8 40.4 + - + +
434D PHE* 3.0 42.3 + - + +
435D GLU 3.3 1.4 + - - +
436D GLY* 1.3 75.0 - - - +
438D GLU* 1.3 63.4 + - - +
439D CYS* 3.2 30.0 + - + -
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Residues in contact with GLU 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D ASP* 4.1 6.4 - - - +
417D VAL* 4.3 17.0 - - + +
418D LYS 4.0 4.0 - - - -
419D THR* 2.4 41.2 + - - +
436D GLY 3.0 21.5 + - - +
437D MET* 1.3 72.6 - - - +
439D CYS* 1.3 60.9 + - - +
440D ARG 4.2 0.2 + - - -
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Residues in contact with CYS 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D SER* 3.3 49.4 - - - -
364D VAL* 4.1 2.2 - - - -
367D ASP* 3.6 11.7 - - - -
417D VAL* 4.2 1.8 - - - +
418D LYS* 3.0 31.8 + - - +
420D ILE* 3.9 14.6 - - + -
437D MET* 3.2 28.1 + - - -
438D GLU* 1.3 74.6 - - - +
440D ARG* 1.3 63.9 + - - +
441D GLY 3.8 2.4 + - - +
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Residues in contact with ARG 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C ARG* 6.2 1.8 - - - +
363D SER 3.6 5.7 - - - +
366D TRP* 3.3 9.5 - - - -
367D ASP* 2.9 33.1 + - - +
371D VAL* 3.5 41.4 - - + +
414D PRO* 3.0 24.3 + - - +
415D ASP* 3.6 40.1 + - - +
416D SER 3.4 4.0 - - - -
417D VAL* 4.2 14.4 - - + +
438D GLU 4.2 0.4 + - - -
439D CYS* 1.3 73.0 - - - +
441D GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D SER* 2.6 30.5 + - - -
366D TRP* 3.8 15.7 - - - -
412D TRP* 3.6 9.2 - - - -
413D ASP 3.6 14.4 - - - -
414D PRO 4.4 0.9 + - - -
416D SER 2.7 13.9 + - - -
418D LYS* 5.6 1.3 - - - +
439D CYS* 3.8 3.2 + - - +
440D ARG* 1.3 73.9 - - - +
442D SER* 1.3 59.9 + - - -
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Residues in contact with SER 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D SER* 3.8 3.4 - - - -
412D TRP* 3.4 14.6 - - - -
413D ASP* 3.2 29.3 + - - +
416D SER* 3.6 13.3 - - - -
418D LYS* 3.5 43.0 + - - +
441D GLY* 1.3 76.0 - - - -
443D PRO* 1.3 74.0 + - - +
444D LEU* 4.9 1.0 - - - +
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Residues in contact with PRO 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ALA 3.7 14.6 - - - +
99D GLY* 3.5 34.8 - - - +
100D GLY* 4.0 1.8 - - - +
363D SER* 4.6 2.9 - - - +
410D VAL* 3.6 22.2 - - + -
411D ILE 3.9 5.2 - - - +
412D TRP* 3.7 9.4 - - + -
418D LYS* 4.6 6.2 + - - -
442D SER* 1.3 93.2 - - - +
444D LEU* 1.3 65.3 + - - +
446D VAL* 3.8 16.2 - - + -
454D LEU* 4.1 9.7 - - + +
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Residues in contact with LEU 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ARG* 3.5 41.3 - - - +
411D ILE* 3.0 20.3 + - + +
413D ASP* 3.6 31.2 - - + +
416D SER* 4.5 2.7 - - - +
418D LYS* 5.1 6.7 - - - +
442D SER* 4.4 4.5 - - - +
443D PRO* 1.3 78.8 - - - +
445D VAL* 1.3 71.7 + - + +
454D LEU* 3.9 17.5 - - - +
455D GLU* 4.1 6.8 - - - -
456D ASP 4.4 4.7 + - - -
457D GLY 5.0 2.3 + - - -
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Residues in contact with VAL 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ILE* 4.5 13.2 - - + -
409D LEU 5.6 0.2 - - - +
410D VAL* 3.3 10.3 - - - +
411D ILE* 2.9 55.7 + - + -
444D LEU* 1.3 86.4 - - + +
446D VAL* 1.3 64.8 - - - +
447D ILE* 4.1 21.5 - - + -
452D ILE* 4.1 14.6 - - + -
454D LEU 3.4 13.2 - - - +
455D GLU* 4.5 14.6 - - + +
456D ASP 5.7 0.4 - - - +
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Residues in contact with VAL 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 3.2 55.0 - - + +
100D GLY* 4.3 4.7 - - - -
102D THR* 4.0 12.3 - - + -
409D LEU 3.9 1.8 - - - -
410D VAL* 4.4 7.0 - - + +
443D PRO* 3.8 13.5 - - + -
445D VAL* 1.3 80.2 - - - +
447D ILE* 1.3 59.5 + - - +
452D ILE* 3.6 3.3 - - - -
453D VAL* 2.8 35.8 + - + +
454D LEU* 3.3 34.7 + - + +
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Residues in contact with ILE 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 4.2 12.6 - - + -
19D ILE* 3.7 32.5 - - + -
37D MET* 4.3 9.4 - - + -
58D ILE* 4.5 3.6 - - + -
102D THR* 3.6 6.6 - - - +
407D ALA 3.4 17.0 - - - +
408D ASP* 3.1 5.5 - - - -
409D LEU* 2.7 46.5 + - + +
411D ILE* 5.7 2.0 - - + -
445D VAL* 4.1 13.9 - - + -
446D VAL* 1.3 75.8 - - - +
448D SER* 1.3 60.8 - - - +
450D GLY* 3.9 18.6 - - - +
451D LYS 3.4 8.1 - - - +
452D ILE* 3.7 21.8 - - + -
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Residues in contact with SER 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D LEU* 3.7 25.4 - - - -
102D THR* 4.2 4.6 + - - -
132D CYS 4.0 14.2 + - - -
133D CYS* 4.2 10.2 - - - +
134D ASP 4.8 1.2 + - - -
408D ASP* 3.6 9.4 + - - -
446D VAL 4.3 0.4 + - - -
447D ILE* 1.3 74.5 - - - +
449D GLN* 1.3 78.9 + - - +
450D GLY 3.2 0.7 - - - -
451D LYS* 2.8 26.6 + - - +
453D VAL* 4.3 11.9 - - - +
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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