Contacts of the strand formed by residues 75 - 81 (chain D) 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 SER 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C GLY* 5.8 0.5 - - - -
64D GLU* 3.5 21.0 + - - -
65D ILE 3.5 2.2 - - - -
66D VAL* 3.7 20.6 - - - +
74D LYS* 1.3 85.4 + - - +
76D VAL* 1.3 67.1 + - - +
77D PRO* 3.8 8.1 - - - +
103D ARG* 4.9 2.3 + - - -
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Residues in contact with VAL 76 (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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18C ILE* 4.0 31.2 - - + +
19C TRP* 3.6 23.8 - - - +
20C GLY* 3.8 26.0 - - - +
113C ILE 4.8 0.4 - - - +
114C SER* 3.6 22.7 - - - -
64D GLU* 3.5 4.3 - - - +
65D ILE 2.8 34.8 + - - +
74D LYS 5.3 1.6 - - - +
75D SER* 1.3 83.6 - - - +
77D PRO* 1.4 65.5 - - + +
78D ILE* 3.4 5.9 - - + +
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Residues in contact with PRO 77 (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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20C GLY* 6.1 0.9 - - - -
21C CYS 6.0 0.4 - - - +
49C THR* 4.3 1.2 + - - -
51C CYS* 4.4 7.8 - - - -
112C TYR* 3.6 55.7 - - + +
113C ILE 5.2 0.2 - - - +
114C SER* 3.8 7.8 - - - -
62D ILE* 3.9 18.6 - - + -
63D VAL 3.7 0.9 - - - +
64D GLU* 3.5 17.7 - - + +
75D SER 3.8 7.0 - - - +
76D VAL* 1.4 96.5 - - + +
78D ILE* 1.3 59.2 + - - +
105D LYS* 4.3 10.3 - - - +
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Residues in contact with ILE 78 (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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18C ILE* 4.6 4.3 - - + -
49C THR* 3.1 34.2 + - - +
51C CYS* 4.4 3.4 - - - -
88C MET* 3.6 2.3 - - - +
114C SER* 4.3 9.0 - - - +
47D LEU* 4.0 28.0 - - + -
50D VAL* 5.0 6.7 - - + -
63D VAL* 2.9 28.9 + - + +
65D ILE* 4.0 24.9 - - + -
76D VAL* 3.4 24.2 - - + +
77D PRO* 1.3 75.0 - - - +
79D ALA* 1.3 63.2 + - - +
91D MET* 4.1 17.0 - - - +
94D ILE* 4.3 10.1 - - + -
102D PHE* 5.3 1.6 - - + -
113D ILE* 6.4 0.7 - - + -
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C CYS* 4.3 2.7 - - - -
88C MET* 3.6 18.6 - - + -
50D VAL* 4.5 22.2 - - + -
61D HIS 3.8 0.3 - - - +
62D ILE* 3.2 8.1 - - - +
63D VAL* 3.1 44.0 + - + +
78D ILE* 1.3 79.7 - - + +
80D THR* 1.3 60.9 + - - +
81D LEU* 4.2 7.0 - - + -
89D ALA* 5.4 0.2 - - + -
91D MET* 4.8 2.9 - - + -
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Residues in contact with THR 80 (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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51C CYS* 3.5 17.2 - - - +
52C LEU* 2.7 30.2 + - + +
53C GLY 5.4 0.7 - - - -
87C PRO* 3.8 36.0 - - + +
88C MET* 3.2 24.8 - - - +
60D PHE* 3.9 20.2 - - + -
61D HIS 3.4 7.6 - - - +
62D ILE* 3.8 12.8 - - + +
79D ALA* 1.3 71.7 + - - +
81D LEU* 1.3 67.5 + - - +
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Residues in contact with LEU 81 (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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87C PRO* 4.7 4.0 - - - -
88C MET* 4.1 8.5 - - - -
50D VAL* 4.0 37.0 - - + +
51D CYS* 4.4 0.2 - - - -
52D LEU* 3.9 33.9 - - + -
59D GLU 3.7 0.2 - - - +
60D PHE* 3.4 5.7 - - - -
61D HIS* 2.8 34.9 + - + +
79D ALA* 4.7 4.3 - - + -
80D THR* 1.3 84.3 - - - +
82D LYS* 1.3 61.7 + - - +
86D LEU* 3.4 23.8 - - + +
87D PRO 4.2 4.5 - - - +
88D MET 3.7 23.1 - - - +
89D ALA* 4.2 1.3 - - + +
111D LEU* 4.7 3.4 - - + -
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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