Contacts of the strand formed by residues 107 - 112 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A HIS 3.4 2.2 + - - -
76A LEU* 3.4 20.1 - - + -
77A ALA 3.2 24.6 + - - +
105A ILE* 3.6 3.0 - - - +
106A GLN* 1.3 81.8 - - + +
108A TYR* 1.3 63.8 + - - +
109A ILE* 3.9 8.0 - - + +
144A PRO 3.4 8.7 - - - -
145A SER* 4.4 2.5 - - - -
146A THR* 2.7 30.3 + - - -
203A ILE* 3.5 34.8 + - + +
204A PHE* 3.8 16.9 + + + +
207A GLY* 3.5 29.3 - - - -
208A PRO* 3.9 16.8 - - + +
211A TRP* 4.3 1.1 - - + -
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Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PHE* 4.3 5.4 - + - -
77A ALA* 3.8 15.7 - - + -
79A ILE* 3.6 32.8 - - + +
92A GLY 4.3 2.8 + - - -
95A LEU* 3.7 7.3 - - - +
96A ALA* 3.6 26.0 + - - +
99A ALA* 3.6 32.1 - - + -
105A ILE* 4.1 9.4 - - + +
107A HIS* 1.3 73.7 - - - +
109A ILE* 1.3 61.9 + - - +
110A TYR* 3.5 17.2 + + + -
134A VAL* 5.9 0.2 - - - +
138A VAL* 3.9 32.6 - - + +
143A LEU* 4.2 13.2 - - + -
144A PRO* 2.8 16.1 + - + +
145A SER* 3.0 28.4 - - - -
146A THR 3.5 0.4 + - - -
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA 2.9 12.5 + - - +
78A PHE* 3.3 14.9 - - + -
79A ILE* 2.8 25.8 + - - +
107A HIS* 4.3 12.8 - - - +
108A TYR* 1.3 72.3 - - - +
110A TYR* 1.3 61.0 + - - +
146A THR* 3.2 15.5 - - - +
148A VAL* 3.9 32.8 - - + -
200A LEU* 4.2 14.1 - - + +
203A ILE* 3.7 30.5 - - + -
204A PHE* 3.4 37.7 - - + -
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Residues in contact with TYR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 3.2 39.0 - - + -
81A THR* 3.9 17.8 + - + -
88A GLU* 4.4 2.6 + - - +
92A GLY* 4.8 2.6 - - - -
108A TYR* 3.5 19.8 + + + -
109A ILE* 1.3 74.1 - - - +
111A SER* 1.3 76.8 + - - +
112A SER* 3.4 4.0 + - - -
131A LYS* 3.5 39.2 - - + +
134A VAL* 3.4 38.1 - - + +
135A GLU* 4.0 4.5 - - - -
138A VAL* 4.9 1.6 - - + -
146A THR 3.1 5.7 + - - -
147A PHE* 3.3 36.6 - + + -
148A VAL* 3.1 23.7 + - - -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLN* 2.6 27.8 + - - -
78A PHE* 3.9 3.8 - - - -
79A ILE 2.8 9.5 + - - -
80A ASN* 3.1 28.8 + - - -
109A ILE 4.1 0.6 + - - -
110A TYR* 1.3 82.4 - - - +
112A SER* 1.3 58.3 + - - +
131A LYS* 3.7 19.2 + - - +
148A VAL* 3.4 23.3 + - - +
150A ALA* 4.9 4.5 + - - +
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TYR* 3.4 12.0 + - - -
111A SER* 1.3 75.4 + - - +
113A MET* 1.3 82.6 + - - +
131A LYS* 3.9 5.9 + - - -
132A PHE* 3.8 16.6 + - - -
135A GLU* 2.9 29.3 + - - +
147A PHE* 4.4 5.8 - - - -
148A VAL 2.6 18.6 + - - +
149A TYR* 3.4 24.5 + - - -
150A 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