Contacts of the strand formed by residues 111 - 118 (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 LEU 111 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G GLU* 3.3 4.3 - - - -
23G LEU* 2.7 60.6 + - + +
50G VAL* 3.9 26.5 - - + -
51G CYS 3.7 4.7 - - - +
52G LEU* 4.0 20.6 - - + -
61G HIS* 4.1 11.2 - - + +
63G VAL* 4.0 17.5 - - + +
79G ALA 5.8 0.2 - - - +
81G LEU* 4.2 4.0 - - + -
104G LEU* 4.0 23.8 - - + -
109G GLY* 4.6 2.2 - - - -
110G PRO* 1.3 75.6 - - - +
112G TYR* 1.3 60.9 + - - +
113G ILE* 3.8 19.3 - - + -
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Residues in contact with TYR 112 (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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21G CYS 3.3 6.7 - - - +
22G GLU* 3.4 37.6 + - + -
50G VAL* 3.4 5.0 - - - +
51G CYS* 2.8 51.0 + - - +
52G LEU 4.3 0.7 - - - -
53G GLY* 3.7 26.6 - - - -
110G PRO* 3.7 19.3 - - + +
111G LEU* 1.3 71.7 - - - +
113G ILE* 1.3 61.1 + - - +
62H ILE* 4.3 9.3 - - + +
77H PRO* 3.4 51.4 - - + +
105H LYS* 3.8 17.8 + - - -
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Residues in contact with ILE 113 (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* 4.2 6.9 - - + -
20G GLY* 3.2 5.7 - - - -
21G CYS* 3.0 41.5 + - - +
23G LEU* 4.2 6.1 - - + -
47G LEU* 3.9 21.5 - - + -
49G THR 3.6 8.1 - - - +
50G VAL* 4.3 12.1 - - + +
63G VAL* 3.6 19.7 - - + -
78G ILE* 5.6 0.7 - - + -
102G PHE* 3.6 41.5 - - + -
111G LEU* 3.8 14.4 - - + -
112G TYR* 1.3 78.0 - - - +
114G SER* 1.3 71.8 + - - +
76H VAL* 4.6 1.4 - - - +
77H PRO 5.1 0.4 - - - -
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Residues in contact with SER 114 (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* 5.6 2.4 - - - +
19G TRP* 3.5 9.2 - - - -
47G LEU* 3.6 12.3 - - - +
48G ARG* 2.9 24.9 + - - +
49G THR* 2.7 42.5 + - - +
113G ILE* 1.3 76.1 - - - +
115G GLY* 1.3 59.1 + - - +
76H VAL* 3.6 23.3 - - - -
77H PRO 3.8 6.7 - - - -
78H ILE* 4.0 9.4 - - - +
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Residues in contact with GLY 115 (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* 3.7 3.9 - - - +
19G TRP* 2.8 45.8 + - - +
45G LEU* 4.8 1.3 - - - -
46G ALA 3.0 14.6 - - - -
47G LEU* 4.1 2.2 - - - -
48G ARG* 3.8 9.1 - - - +
114G SER* 1.3 79.1 + - - +
116G GLN* 1.3 62.6 + - - +
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Residues in contact with GLN 116 (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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16G ASP 3.0 21.3 + - - +
17G LEU 3.4 8.7 + - - +
18G ILE* 3.6 17.1 - - + +
19G TRP 4.6 0.9 - - - +
44G GLN 3.7 0.5 - - - +
45G LEU* 3.7 5.5 - - - +
46G ALA* 2.9 32.9 + - - +
48G ARG* 3.1 25.2 + - + +
115G GLY* 1.3 77.2 - - - +
117G HIS* 1.3 68.7 + - - +
118G VAL* 3.4 2.0 + - + -
93H GLY 3.0 25.5 - - - +
94H ILE* 3.4 4.9 - - - -
95H GLU* 2.7 32.5 + - - +
96H LEU* 4.1 10.5 - - - +
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Residues in contact with HIS 117 (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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16G ASP* 3.3 28.0 + - - +
17G LEU* 3.2 41.6 + - + +
18G ILE 5.3 0.4 - - - -
19G TRP* 4.1 21.4 - - + +
32G PHE* 3.6 38.4 - + - -
34G VAL* 5.2 7.3 - - + +
43G HIS* 4.9 23.2 - + + +
44G GLN 3.5 8.2 + - - +
45G LEU* 5.0 2.0 - - + +
116G GLN* 1.3 72.8 - - - +
118G VAL* 1.4 58.4 + - - +
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Residues in contact with VAL 118 (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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16G ASP 5.5 0.9 - - - +
43G HIS* 3.3 9.2 - - - +
44G GLN* 2.9 40.6 + - + +
46G ALA* 4.2 11.9 - - + -
48G ARG* 4.3 20.6 - - - +
95G GLU* 3.0 32.5 - - + +
116G GLN* 5.0 1.8 - - + +
117G HIS* 1.4 72.1 - - - +
119G ALA* 1.4 78.0 + - + +
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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