Contacts of the strand formed by residues 124 - 129 (chain B) in PDB entry 3VTW
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 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 4.4 3.8 - - + -
47B PRO 3.0 12.3 + - - +
48B VAL* 3.4 6.9 - - + +
49B ILE* 3.0 24.6 + - - +
98B VAL* 4.1 14.4 - - + -
110B ILE* 3.9 17.3 - - + -
113B VAL* 3.9 14.8 - - + +
114B TYR* 3.9 35.2 - - + +
117B GLU* 3.9 35.7 - - + +
118B LYS* 4.4 3.4 - - - +
122B GLY 4.0 0.4 + - - -
123B PHE* 1.3 72.7 - - - +
125B TYR* 1.3 63.3 + - - +
126B MET* 3.7 27.4 - - + -
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PHE* 3.4 25.4 - + + -
23B LYS* 3.7 20.0 - - + +
31B ARG* 3.7 3.8 - - - -
49B ILE* 3.5 35.7 - - + -
51B GLU* 4.4 10.3 - - - -
97B LEU 4.1 1.9 - - - +
98B VAL* 4.0 19.6 - - - +
99B ASN* 4.6 15.2 + - - +
117B GLU 5.1 2.8 + - - -
119B ASP* 3.5 40.4 - - + +
121B ASP* 2.9 25.2 + - - -
123B PHE* 3.6 9.5 + - + -
124B LEU* 1.3 74.5 - - - +
126B MET* 1.3 69.4 + - - +
127B VAL* 5.5 2.7 - - + -
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B VAL* 3.2 31.2 - - + -
49B ILE 2.8 15.2 + - - +
50B ILE* 4.1 8.1 - - + -
51B GLU* 3.0 28.0 + - - +
75B MET* 4.3 10.5 - - - +
78B LEU* 3.8 19.1 - - + -
96B LEU* 3.8 38.4 - - + -
97B LEU 3.4 6.7 - - - +
98B VAL* 3.9 14.1 - - + -
110B ILE* 4.1 5.4 - - + -
124B LEU* 3.7 22.7 - - + -
125B TYR* 1.3 82.9 - - - +
127B VAL* 1.3 67.6 + - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU* 3.3 10.8 - - + +
52B ARG 4.1 1.1 - - - +
53B TYR* 3.4 44.4 - - + +
96B LEU* 3.4 3.5 - - - -
97B LEU* 2.6 54.0 + - + +
125B TYR* 5.5 2.2 - - + -
126B MET* 1.3 81.8 - - - +
128B TYR* 1.3 63.3 + - - +
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Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 3.8 16.4 - - + -
51B GLU 3.1 18.3 + - - -
52B ARG* 3.5 34.2 - - + +
53B TYR* 3.0 22.6 + - - +
59B LEU* 3.9 22.0 - - + -
60B PRO 2.3 31.3 + - - -
61B VAL* 3.3 2.3 - - - -
62B LEU* 3.2 41.2 + - + -
82B ILE* 4.9 0.4 - - + -
86B LEU* 3.9 13.8 - - + +
94B PHE* 3.8 24.0 - + + -
95B PHE 3.1 10.1 - - - +
96B LEU* 4.0 4.9 - - + -
127B VAL* 1.3 76.4 - - - +
129B ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B TYR* 4.0 11.2 - - + -
56B GLU* 3.4 12.3 - - - +
59B LEU* 3.5 8.4 - - - +
94B PHE* 3.5 4.0 - - - -
95B PHE* 2.9 31.6 + - - -
97B LEU* 4.1 3.8 - - + +
128B TYR* 1.3 76.9 - - - +
130B SER* 1.3 61.4 + - - +
131B GLN 3.3 20.2 - - - +
134B PHE* 4.0 21.1 - - + -
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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