Contacts of the strand formed by residues 116 - 121 (chain B) in PDB entry 2V5Q
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 PHE 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 3.8 31.4 - - + -
105B HIS* 3.7 48.9 - + + +
106B ARG* 3.4 31.2 - - + +
108B LEU 4.9 6.7 + - - +
114B VAL 3.5 1.0 + - - -
115B GLY* 1.3 72.3 - - - -
117B HIS* 1.3 63.2 + - - +
118B GLY* 3.6 33.9 - - - -
119B PHE* 4.1 10.3 - + + -
128B VAL* 3.7 18.2 - - + -
129B VAL 4.0 1.6 - - - -
130B LEU* 3.8 11.4 - - + -
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Residues in contact with HIS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 5.6 2.2 + - - -
77B GLU* 5.9 1.1 - - - -
79B PHE* 3.6 27.6 - + + -
115B GLY* 3.9 11.0 - - - -
116B PHE* 1.3 80.5 + - - +
118B GLY* 1.3 58.0 + - - +
129B VAL* 2.8 27.1 + - + +
130B LEU 3.9 0.2 - - - -
131B GLU* 3.7 34.4 - - - +
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Residues in contact with GLY 118 (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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116B PHE* 3.6 20.4 - - - -
117B HIS* 1.3 80.3 - - - +
119B PHE* 1.3 59.8 + - - +
120B PHE* 5.2 0.7 - - - -
128B VAL* 3.7 0.9 - - - -
129B VAL* 2.8 36.9 + - - +
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASP* 4.2 5.4 + - - +
102B ILE* 3.7 36.3 - - + -
106B ARG* 3.5 33.4 - - - -
116B PHE* 4.1 13.7 - + + -
118B GLY* 1.3 73.8 - - - +
120B PHE* 1.3 81.3 + - - +
121B GLU* 4.6 13.2 - - + -
126B VAL* 4.6 6.7 - - + -
127B PHE 3.2 14.8 - - - +
128B VAL* 4.3 9.4 - - + -
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.1 9.4 - - + -
45B VAL 3.5 35.2 - - - -
46B ASP* 3.6 33.7 - - + +
47B PRO* 4.1 6.5 - - + -
53B TYR* 3.6 39.3 - + - -
118B GLY 5.2 0.2 - - - -
119B PHE* 1.3 87.9 - - - +
121B GLU* 1.3 68.4 + - - +
126B VAL* 3.8 3.8 - - - +
127B PHE* 2.8 59.3 + + + +
129B VAL* 3.8 17.7 - - + -
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Residues in contact with GLU 121 (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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45B VAL 5.0 0.9 - - - +
47B PRO* 4.0 21.5 - - - +
86B LYS* 2.7 33.2 + - - +
119B PHE* 4.6 15.2 - - + -
120B PHE* 1.3 82.7 - - - +
122B ASP* 1.3 61.6 + - - +
125B PHE 3.3 16.2 - - - +
126B VAL* 4.2 11.8 - - + +
127B PHE* 3.9 6.3 - - - -
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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