Contacts of the strand formed by residues 107 - 112 (chain G) in PDB entry 2VUU
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 HIS 107 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75G HIS 3.4 1.6 + - - -
76G LEU* 3.5 18.6 - - + -
77G ALA 3.2 23.0 + - - -
105G ILE* 3.6 2.9 - - - -
106G GLN* 1.3 80.6 - - + +
108G TYR* 1.3 63.4 + - - +
109G ILE* 3.9 5.7 - - + +
144G PRO 3.4 6.5 + - - -
145G SER 4.7 0.7 - - - -
146G THR* 2.9 34.5 - - - -
203G ILE* 3.5 19.6 + - + +
204G PHE* 3.4 33.2 - + + -
207G GLY* 3.5 17.4 + - - -
208G PRO* 3.5 33.5 - - + +
211G TRP* 4.5 0.8 - - + -
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Residues in contact with TYR 108 (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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71G PHE* 4.4 6.1 - + - -
77G ALA* 3.7 13.9 - - + -
79G ILE* 3.4 34.7 - - + +
92G GLY 4.5 2.1 + - - -
95G LEU* 3.8 7.6 - - - +
96G ALA* 3.6 23.8 + - + +
99G ALA* 3.5 33.7 - - + -
105G ILE* 3.8 11.4 - - + -
107G HIS* 1.3 73.9 + - - +
109G ILE* 1.3 61.2 + - - +
110G TYR* 3.6 21.0 + + + -
134G VAL* 6.1 0.2 - - - +
138G VAL* 4.2 21.0 - - + +
143G LEU* 3.8 18.2 - - + -
144G PRO 2.7 16.8 + - - +
145G SER* 2.9 30.8 - - - -
146G THR 3.4 0.5 + - - -
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Residues in contact with ILE 109 (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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77G ALA 2.8 12.0 + - - +
78G PHE* 3.4 19.5 - - + -
79G ILE* 2.8 27.4 + - - +
107G HIS* 4.2 11.0 - - + +
108G TYR* 1.3 73.6 - - - +
110G TYR* 1.3 59.9 + - - +
146G THR* 3.3 15.0 - - - +
148G VAL* 3.9 23.8 - - + -
200G LEU* 4.0 14.4 - - + +
203G ILE* 3.5 33.4 - - + -
204G PHE* 3.5 36.8 - - + -
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Residues in contact with TYR 110 (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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79G ILE* 3.5 34.1 - - + +
81G THR* 4.0 16.5 + - + -
88G GLU* 4.9 1.0 + - - +
92G GLY* 5.2 1.3 - - - -
108G TYR* 3.6 17.8 + + + -
109G ILE* 1.3 74.5 - - - +
111G SER* 1.3 78.0 + - - +
112G SER* 3.3 13.1 + - - -
131G LYS* 3.3 38.8 - - + +
134G VAL* 3.4 40.3 - - + +
135G GLU* 4.4 3.8 - - - -
138G VAL* 4.8 1.6 - - + -
146G THR 3.1 6.5 + - - -
147G PHE* 3.3 31.6 - + + -
148G VAL* 3.1 24.0 + - - -
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Residues in contact with SER 111 (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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17G GLN* 2.7 25.8 + - - -
78G PHE* 4.1 8.6 - - - -
79G ILE 2.8 16.5 + - - +
80G ASN* 3.1 22.3 + - - -
109G ILE 4.1 0.4 + - - -
110G TYR* 1.3 85.7 - - - +
112G SER* 1.3 59.7 + - - +
113G MET* 5.8 0.2 - - - -
131G LYS* 3.8 14.3 + - - +
148G VAL* 3.5 17.2 + - - +
150G ALA* 5.0 6.6 + - - +
218G LEU* 5.9 0.5 - - - +
1353G NAP 6.0 0.3 - - - -
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Residues in contact with SER 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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110G TYR* 3.3 20.8 + - - -
111G SER* 1.3 75.0 + - - +
113G MET* 1.3 82.6 + - - +
131G LYS* 3.6 16.3 + - - -
132G PHE* 3.7 2.8 - - - -
135G GLU* 3.0 28.2 + - - +
147G PHE* 4.4 1.6 - - - -
148G VAL 2.8 18.9 + - - +
149G TYR* 3.4 27.7 + - - -
150G ALA 4.3 0.7 + - - -
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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