Contacts of the strand formed by residues 72 - 81 (chain I) in PDB entry 2VTX
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 ALA 72 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68I GLN* 3.5 6.7 - - - -
69I GLU 2.9 36.5 + - - +
70I GLU 3.5 1.2 + - - +
71I GLY* 1.3 73.4 - - - +
73I GLU* 1.3 67.4 + - - +
74I LYS* 5.4 0.4 - - + -
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Residues in contact with GLU 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I VAL* 3.3 28.4 - - + +
67I ASP 3.6 6.9 - - - +
68I GLN* 3.8 23.0 + - - +
72I ALA* 1.3 75.3 - - - +
74I LYS* 1.3 61.5 + - - +
75I SER* 4.0 3.1 + - - +
103I ARG* 3.6 20.3 + - - -
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Residues in contact with LYS 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H ILE* 3.9 24.8 - - + +
65I ILE 3.5 0.9 - - - +
66I VAL* 3.1 10.5 - - - +
67I ASP 2.7 38.9 + - - +
69I GLU* 5.0 11.0 - - + +
72I ALA 3.4 3.9 + - - +
73I GLU* 1.3 72.3 - - - +
75I SER* 1.3 60.2 + - - +
76I VAL* 4.3 2.9 - - + -
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Residues in contact with SER 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H GLY* 5.9 0.2 - - - -
64I GLU* 3.5 21.2 + - - -
65I ILE 3.3 2.0 - - - -
66I VAL* 3.2 27.0 - - - +
73I GLU* 4.0 4.2 + - - +
74I LYS* 1.3 71.2 + - - +
76I VAL* 1.3 64.7 + - - +
77I PRO* 3.5 8.9 - - - +
103I ARG* 4.2 5.4 + - - -
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Residues in contact with VAL 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H ILE* 3.4 39.0 - - + -
19H TRP* 3.4 22.7 - - - +
20H GLY* 3.9 11.2 - - - +
113H ILE 4.6 0.4 - - - +
114H SER* 3.4 33.0 - - - -
115H GLY 5.4 0.2 - - - +
64I GLU* 3.7 3.5 - - - +
65I ILE* 2.8 34.5 + - + +
74I LYS* 4.9 2.2 - - + -
75I SER* 1.3 78.3 - - - +
77I PRO* 1.3 68.2 - - + +
78I ILE* 3.3 10.9 - - + +
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Residues in contact with PRO 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H GLY* 6.2 0.9 - - - -
49H THR* 4.3 0.3 + - - -
51H CYS* 4.2 11.0 - - - -
112H TYR* 3.6 54.2 - - + +
113H ILE 4.9 0.9 - - - +
114H SER* 3.7 13.7 + - - -
62I ILE* 4.3 9.6 - - + -
63I VAL 3.5 7.6 - - - +
64I GLU* 3.7 5.6 - - + +
75I SER 3.5 10.3 - - - +
76I VAL* 1.3 85.7 - - + +
78I ILE* 1.3 60.5 + - - +
105I LYS* 4.1 21.8 - - + -
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Residues in contact with ILE 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49H THR* 3.1 40.4 + - + +
51H CYS* 4.2 4.7 - - - -
88H MET* 3.8 4.2 - - - +
114H SER* 4.2 9.4 - - - +
47I LEU* 3.8 23.1 - - + -
50I VAL* 5.4 2.9 - - + -
63I VAL* 2.9 26.4 + - + +
65I ILE* 3.5 36.6 - - + -
76I VAL* 3.3 22.9 - - + +
77I PRO* 1.3 73.8 - - - +
79I ALA* 1.3 70.9 + - + +
91I MET* 4.4 7.9 - - - +
94I ILE* 4.2 12.1 - - + -
102I PHE* 5.1 1.6 - - + -
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Residues in contact with ALA 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H CYS* 4.0 4.1 - - - -
88H MET* 3.7 18.6 - - + -
50I VAL* 4.3 19.7 - - + -
61I HIS 3.5 1.1 - - - +
62I ILE* 3.1 5.8 - - - +
63I VAL* 2.7 51.6 + - + +
77I PRO 3.9 0.8 - - - -
78I ILE* 1.3 84.4 - - + +
80I THR* 1.3 60.9 + - - +
81I LEU* 4.9 3.1 - - + -
89I ALA* 5.2 0.4 - - + -
91I MET* 4.9 3.8 - - + -
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Residues in contact with THR 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H CYS* 3.6 14.8 - - - +
52H LEU* 2.7 29.5 + - + +
53H GLY 5.4 0.9 - - - +
87H PRO* 3.8 29.6 - - + +
88H MET* 3.3 26.2 - - - +
60I PHE* 3.8 25.4 - - + -
61I HIS 3.3 4.9 - - - +
62I ILE* 3.5 18.7 - - + +
79I ALA* 1.3 72.8 - - - +
81I LEU* 1.4 66.8 + - - +
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Residues in contact with LEU 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H PRO* 4.6 4.3 - - - -
88H MET* 4.1 8.3 - - - -
50I VAL* 3.6 35.4 - - + +
51I CYS* 4.3 0.9 - - - -
52I LEU* 4.0 23.8 - - + -
59I GLU 3.6 0.2 - - - +
60I PHE* 3.4 4.6 - - - -
61I HIS* 2.7 35.7 + - + +
79I ALA* 4.9 1.6 - - + -
80I THR* 1.4 84.9 - - - +
82I LYS* 1.3 62.6 + - - +
86I LEU* 3.2 23.8 - - + +
87I PRO 4.0 15.9 - - - +
88I MET 3.6 25.6 - - - +
89I ALA* 4.1 3.1 - - + +
111I LEU* 4.6 3.6 - - + -
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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