Contacts of the strand formed by residues 113 - 118 (chain B) in PDB entry 2XCF
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 VAL 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ALA 5.2 0.7 - - - +
2A PRO* 3.9 19.3 - - + -
105B TYR* 3.8 32.5 - - + -
106B LEU 3.4 4.7 - - - +
107B VAL* 4.5 7.6 - - + -
111B ALA 4.4 2.7 - - - +
112B ASP* 1.3 79.3 - - - +
114B ILE* 1.3 64.7 + - - +
115B PRO* 3.6 8.8 - - + +
130B ARG* 5.9 0.9 + - - -
134B TYR* 5.7 0.2 + - - -
34C LYS* 6.0 1.6 - - + -
35C PRO* 3.8 35.2 - - + -
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Residues in contact with ILE 114 (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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105B TYR* 3.5 1.5 - - - -
106B LEU* 2.8 46.6 + - + +
108B THR* 3.6 21.5 - - + -
113B VAL* 1.3 77.8 - - - +
115B PRO* 1.3 76.6 - - + +
116B VAL* 3.6 9.3 - - + +
126B LEU* 3.9 24.7 - - + -
128B SER 5.3 2.7 - - - +
130B ARG* 4.6 10.3 - - + +
134B TYR* 3.5 33.4 - - + +
135B LEU* 3.6 25.6 - - + -
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Residues in contact with PRO 115 (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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104B LEU 3.5 7.6 - - - +
105B TYR* 3.9 23.1 - - + -
113B VAL* 3.6 10.1 - - + +
114B ILE* 1.3 89.6 - - + +
116B VAL* 1.3 64.1 + - - +
126B LEU* 3.5 2.9 - - - -
127B LEU* 3.1 46.8 + - + -
128B SER* 4.9 2.6 + - - +
130B ARG* 6.2 2.5 - - - +
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Residues in contact with VAL 116 (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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102B SER 3.6 0.5 - - - +
103B ASP* 3.9 1.6 - - - -
104B LEU* 2.8 46.9 + - + +
106B LEU* 4.3 14.8 - - + +
114B ILE* 3.6 13.9 - - + +
115B PRO* 1.3 80.3 - - - +
117B ARG* 1.3 65.5 - - - +
124B GLY* 3.6 12.6 - - - -
125B SER 3.4 24.9 - - - +
126B LEU* 4.0 18.6 - - + -
127B LEU* 4.4 3.1 - - - -
143B LEU* 4.3 11.7 - - + -
167B VAL* 4.1 11.0 - - + -
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Residues in contact with ARG 117 (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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102B SER* 3.5 32.3 + - - -
103B ASP* 3.0 29.1 + - - +
116B VAL* 1.3 74.4 - - - +
118B ARG* 1.3 67.2 + - - +
119B ARG* 3.6 35.7 + - - +
124B GLY* 3.1 2.6 - - - -
125B SER* 2.8 35.5 + - - +
127B LEU* 3.9 18.2 - - + +
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Residues in contact with ARG 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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100B GLY* 5.7 5.3 + - - -
101B SER 4.6 10.5 + - - -
102B SER* 2.9 41.5 + - - +
104B LEU* 3.9 19.9 - - + +
116B VAL 3.9 0.4 + - - -
117B ARG* 1.3 80.6 + - - +
119B ARG* 1.3 71.5 + - - +
120B GLY 3.1 20.2 + - - +
121B ASP* 2.6 34.7 + - - +
123B ARG 3.8 7.2 - - - +
124B GLY* 4.1 2.0 - - - -
151B VAL* 4.2 15.6 + - - +
169B PHE* 3.8 14.2 - - + -
171B PRO* 4.4 8.9 - - - +
173B GLU* 5.0 6.7 + - - -
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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