Contacts of the strand formed by residues 44 - 52 (chain G) 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 GLN 44 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32G PHE* 5.3 2.5 - - - -
42G GLU 4.9 2.0 - - - +
43G HIS* 1.3 77.0 - - - +
45G LEU* 1.3 64.7 + - - +
46G ALA 3.8 0.4 - - - -
95G GLU* 3.3 38.5 + - + +
96G LEU 3.3 14.1 - - - +
97G ASP* 3.0 23.0 + - - +
98G PRO* 5.0 1.3 - - - -
117G HIS* 3.5 7.1 + - - -
118G VAL* 2.9 35.1 + - + -
119G ALA* 3.3 26.6 - - + +
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Residues in contact with LEU 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G TRP* 3.7 38.6 - - + -
32G PHE* 3.9 42.8 - - + -
44G GLN* 1.3 72.4 - - - +
46G ALA* 1.3 59.4 + - - +
47G LEU* 3.8 14.6 + - + -
94G ILE 3.5 1.9 - - - +
95G GLU* 3.3 2.4 - - - -
96G LEU* 2.7 45.9 + - + +
98G PRO* 4.8 0.8 - - - +
100G VAL* 4.0 7.0 - - + -
102G PHE* 3.8 32.3 - - + -
116G GLN 3.7 13.9 - - - +
117G HIS* 5.0 1.8 - - + +
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Residues in contact with ALA 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G GLN 3.8 2.2 + - - -
45G LEU* 1.3 71.5 - - - +
47G LEU* 1.3 61.9 + - - +
48G ARG* 3.5 32.0 - - - +
94G ILE 3.2 6.1 - - - +
95G GLU* 3.7 22.0 - - + -
115G GLY* 3.0 4.0 - - - -
116G GLN 2.9 38.3 + - - +
118G VAL* 4.2 11.7 - - + -
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Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G TRP* 4.5 3.1 - - + -
45G LEU* 3.8 17.9 + - + -
46G ALA* 1.3 75.1 - - - +
48G ARG* 1.3 70.7 + - - +
50G VAL* 5.8 0.2 - - + -
78G ILE* 3.8 28.0 - - + -
91G MET* 3.8 30.1 - - + +
92G VAL* 5.3 0.2 - - - -
93G GLY 5.3 1.0 + - - -
94G ILE* 2.8 32.6 + - + +
96G LEU* 4.0 22.0 - - + -
102G PHE* 3.8 27.4 - - + -
113G ILE* 3.9 12.3 - - + -
114G SER 3.6 12.8 - - - +
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Residues in contact with ARG 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ILE* 5.3 2.0 - - + -
46G ALA* 3.5 30.8 - - - +
47G LEU* 1.3 80.4 + - - +
49G THR* 1.3 72.0 + - - +
90G THR* 3.7 4.9 - - - +
91G MET* 3.0 26.1 + - - +
93G GLY 5.7 4.9 - - - +
114G SER* 2.9 20.1 + - - +
115G GLY* 3.8 17.3 - - - -
116G GLN* 3.1 24.7 + - + +
118G VAL* 4.3 12.9 - - - +
92H VAL 3.5 18.1 + - - +
93H GLY* 2.9 34.4 + - - -
94H ILE* 3.8 22.7 - - + -
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Residues in contact with THR 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ARG* 1.3 93.9 - - + +
50G VAL* 1.3 73.1 + - - +
51G CYS* 5.0 0.7 - - - +
88G MET* 4.4 2.9 - - + -
89G ALA 3.3 12.1 - - - +
90G THR* 4.5 5.4 - - + +
91G MET* 4.4 3.5 - - - +
113G ILE* 3.6 0.5 - - - +
114G SER* 2.7 48.5 + - - +
77H PRO 4.3 0.9 + - - -
78H ILE* 3.0 32.9 + - - +
91H MET* 4.4 18.2 - - + -
92H VAL 6.2 0.4 - - - +
94H ILE* 4.4 11.2 - - + -
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Residues in contact with VAL 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G THR* 1.3 80.2 - - - +
51G CYS* 1.3 67.5 + - - +
63G VAL* 4.1 18.8 - - + -
78G ILE* 5.1 4.5 - - + -
79G ALA* 4.6 6.3 - - + -
81G LEU* 3.7 20.9 - - + -
88G MET* 3.3 1.4 - - - +
89G ALA* 3.0 32.9 + - + +
91G MET* 3.9 25.1 - - + -
111G LEU* 3.9 24.0 - - + -
112G TYR 3.4 11.0 - - - +
113G ILE* 4.3 15.7 - - + -
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Residues in contact with CYS 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G THR* 5.0 1.1 - - - +
50G VAL* 1.3 78.7 - - - +
52G LEU* 1.3 59.3 + - - +
81G LEU* 4.5 2.0 - - - -
87G PRO 3.6 5.6 - - - -
88G MET* 3.6 12.6 - - + -
111G LEU* 3.7 1.9 - - - +
112G TYR* 2.8 42.5 + - - +
62H ILE* 5.0 0.9 - - - -
77H PRO* 3.9 28.9 - - - -
78H ILE 4.2 6.1 - - - +
79H ALA* 4.0 18.6 - - - +
80H THR* 3.2 22.2 - - - +
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Residues in contact with LEU 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G CYS* 1.3 73.1 - - - +
53G GLY* 1.3 64.1 + - - +
56G ALA* 4.8 2.0 - - + -
61G HIS* 3.5 41.1 - - + +
81G LEU* 4.1 9.9 - - + -
82G LYS* 3.7 14.6 - - - +
83G PRO* 3.4 47.8 - - + -
87G PRO* 2.9 23.0 + - + +
110G PRO 3.8 7.4 - - - +
111G LEU* 4.0 15.5 - - + -
112G TYR* 4.3 2.7 - - - -
62H ILE* 3.5 1.7 - - - +
80H THR* 2.5 36.2 + - + +
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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