Contacts of the strand formed by residues 125 - 130 (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 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLU* 3.7 37.9 - - + -
40B ILE* 3.7 30.3 - - + -
41B PRO* 4.0 14.1 - - + -
83B ILE* 3.5 20.4 - - + -
84B VAL 3.2 4.9 - - - +
85B PRO* 3.6 30.5 - - + -
86B LYS* 3.8 4.2 - - - +
121B GLU* 3.3 6.9 - - - +
122B ASP* 2.8 33.7 + - - +
124B ASP* 1.3 105.4 - - + +
126B VAL* 1.3 62.4 + - - +
127B PHE* 3.6 21.6 - + + -
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS 3.6 1.9 - - - +
83B ILE* 3.6 4.2 - - - +
84B VAL* 2.8 39.0 + - + +
86B LYS* 4.0 18.2 - - + -
89B LEU* 4.0 20.4 - - + -
98B MET* 4.4 25.4 - - + -
102B ILE* 4.4 10.1 - - + -
119B PHE* 4.6 8.3 - - + -
120B PHE 3.8 9.6 - - - +
121B GLU* 4.3 10.3 - - + +
125B PHE* 1.3 74.9 - - - +
127B PHE* 1.3 65.6 + - - +
128B VAL* 4.4 10.0 - - + +
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 4.5 3.8 - - + -
41B PRO* 4.5 7.4 - - + -
44B LEU* 3.7 35.9 - - + -
45B VAL 5.4 3.4 - - - -
81B GLY* 6.5 0.9 - - - -
82B LYS 3.6 3.1 - - - -
83B ILE* 3.7 24.0 - - + -
119B PHE* 3.2 7.8 - - - +
120B PHE* 2.8 79.6 + + + +
121B GLU* 3.9 2.9 - - - -
122B ASP* 3.6 43.3 - - + -
125B PHE* 3.6 24.5 - + + -
126B VAL* 1.3 72.2 - - - +
128B VAL* 1.3 62.1 + - - +
129B VAL* 4.2 1.5 + - + -
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA 3.4 2.1 - - - +
81B GLY* 3.4 4.6 - - - -
82B LYS* 2.8 55.7 + - + +
84B VAL* 5.8 1.3 - - + -
98B MET* 4.5 10.1 - - + -
102B ILE* 4.2 26.5 - - + -
116B PHE* 3.7 22.0 - - + -
118B GLY 3.8 2.7 - - - +
119B PHE* 4.3 2.2 - - + -
126B VAL* 4.4 7.4 - - + +
127B PHE* 1.3 79.0 - - - +
129B VAL* 1.3 64.1 - - - +
130B LEU* 3.7 29.6 + - + +
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Residues in contact with VAL 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* 4.2 15.7 - - + +
70B ILE* 4.0 18.2 - - + -
79B PHE* 3.6 41.5 - - + -
80B ALA 3.6 2.7 - - - -
116B PHE* 3.8 0.5 - - - -
117B HIS* 2.8 40.4 + - + -
118B GLY* 2.8 24.8 + - - +
120B PHE* 3.8 30.1 - - + -
127B PHE* 5.2 1.1 - - + -
128B VAL* 1.3 73.2 - - - +
130B LEU* 1.3 58.6 + - - +
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Residues in contact with LEU 130 (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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79B PHE* 3.4 9.5 - - - +
80B ALA* 2.8 41.2 + - + +
82B LYS* 4.4 28.5 - - + -
105B HIS* 3.7 31.0 - - + +
114B VAL* 3.9 13.5 - - + -
115B GLY 3.4 7.9 - - - +
116B PHE* 3.8 14.8 - - + -
117B HIS* 3.9 5.2 - - - -
128B VAL* 3.7 26.7 - - + +
129B VAL* 1.3 74.4 - - - +
131B GLU* 1.3 64.3 + - - +
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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