Contacts of the strand formed by residues 53 - 60 (chain M) in PDB entry 2VGL
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 53 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M ILE* 5.0 2.0 - - + -
28M ALA* 4.9 7.4 - - + +
49M ASN* 3.7 3.9 + - - -
50M ILE 3.0 30.8 + - - -
51M ALA* 3.1 8.4 + - - +
52M ARG* 1.3 75.4 - - - +
54M SER* 1.3 61.6 + - - +
55M PHE* 3.1 21.1 - - + -
68M VAL* 3.5 29.4 - - + -
69M THR 3.8 11.4 - - - +
70M LYS* 3.0 30.5 + - + -
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Residues in contact with SER 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B LEU* 3.7 25.4 - - - +
574B TYR* 2.8 28.1 + - - -
581B PHE* 4.8 2.6 - - - -
47M VAL* 5.0 0.4 - - - -
48M THR 3.5 4.0 - - - -
49M ASN* 2.8 17.9 + - - +
52M ARG 4.2 0.4 + - - -
53M THR* 1.3 70.6 - - - +
55M PHE* 1.3 60.3 + - - +
56M PHE* 4.3 8.5 - - - -
68M VAL* 3.4 12.3 - - - +
69M THR 2.9 35.0 + - - -
71M GLN 5.4 0.4 - - - -
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Residues in contact with PHE 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M ALA* 3.5 30.7 - - - -
31M ALA* 3.9 16.6 - - + -
32M PHE* 3.5 41.3 - + + -
36M VAL* 5.4 2.5 - - + -
46M PRO 3.3 2.4 - - - +
47M VAL* 3.2 8.1 - - - +
48M THR* 2.9 42.7 + - - +
50M ILE* 4.2 16.8 - - + -
53M THR* 3.1 48.5 - - + -
54M SER* 1.3 73.4 - - - +
56M PHE* 1.3 63.9 + - - +
57M HIS* 5.1 1.7 + - - -
66M ALA* 5.8 0.4 - - + -
67M ALA 3.5 2.5 - - - +
68M VAL* 3.6 27.6 - - + -
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Residues in contact with PHE 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570B LEU* 3.7 33.9 - - + -
32M PHE* 4.6 0.9 - - - -
46M PRO 3.5 5.8 - - - -
47M VAL* 4.1 13.2 - - + -
54M SER* 4.5 7.9 - - - -
55M PHE* 1.3 80.9 - - - +
57M HIS* 1.3 65.3 + - - +
66M ALA* 3.2 3.5 - - - +
67M ALA* 2.7 41.4 + - + +
68M VAL 4.8 0.4 - - - -
69M THR* 4.4 13.7 - - - -
73M VAL* 4.4 6.5 - - + -
75M ALA* 3.8 20.6 - - + -
78M VAL* 3.3 52.5 - - + -
79M PHE* 3.7 22.9 - + + -
82M LEU* 4.5 2.7 - - + -
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Residues in contact with HIS 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU* 4.2 6.6 - - - +
32M PHE* 3.6 22.3 - + + -
36M VAL* 3.7 26.6 - - + +
44M ARG* 3.0 38.1 + - + -
45M SER 3.8 20.4 + - - -
46M PRO* 3.4 18.5 + - + +
48M THR* 5.6 1.4 + - - -
55M PHE 5.1 1.2 + - - -
56M PHE* 1.3 77.2 - - - +
58M VAL* 1.3 67.8 + - - +
64M TRP* 3.6 18.6 - + + -
65M LEU 3.0 16.6 - - - +
66M ALA* 4.1 0.4 - - - +
79M PHE* 3.8 16.3 - - - -
82M LEU* 4.4 3.3 - - - +
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Residues in contact with VAL 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLU* 4.1 16.4 - - + +
44M ARG* 5.8 0.2 - - - +
57M HIS* 1.3 82.2 - - - +
59M LYS* 1.3 63.6 + - - +
60M ARG* 2.9 46.8 + - + +
64M TRP* 3.7 1.9 - - - -
65M LEU* 2.8 38.3 + - + +
79M PHE* 4.5 7.2 - - + -
82M LEU* 4.4 16.3 - - + +
83M TYR* 3.6 31.4 - - + -
86M CYS* 5.0 5.2 - - - -
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Residues in contact with LYS 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B GLU* 5.1 2.8 + - - -
44M ARG* 4.3 15.9 - - - +
57M HIS* 4.3 2.6 - - - -
58M VAL* 1.3 79.7 - - - +
60M ARG* 1.3 71.4 + - - +
61M SER 3.1 29.0 + - - +
62M ASN* 4.9 3.5 - - - +
63M ILE 3.5 7.0 - - - +
64M TRP* 3.9 48.2 - - + +
218M ASP* 3.1 38.7 + - - +
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Residues in contact with ARG 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 3.5 23.8 + - - -
297B GLU* 4.8 5.3 + - - -
58M VAL* 2.9 33.0 + - + +
59M LYS* 1.3 78.9 + - - +
61M SER* 1.3 63.0 + - - +
63M ILE* 2.7 41.3 + - + +
65M LEU* 4.4 6.5 - - + +
83M TYR* 4.0 15.3 - - - -
86M CYS* 3.8 30.5 - - - +
96M ILE* 3.3 26.9 - - + +
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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
------------------------------------------------------------
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