Contacts of the strand formed by residues 110 - 115 (chain A) in PDB entry 1CW0
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 ARG 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TYR* 3.0 27.7 + - - +
58A ARG* 3.2 12.5 + - + +
59A CYS* 3.2 13.4 - - + +
60A VAL* 2.9 26.5 + - - +
105A GLN* 5.6 0.2 - - - -
108A GLY 4.0 2.2 + - - +
109A TRP* 1.3 73.0 - - - +
111A VAL* 1.3 60.3 + - - +
137A TRP* 2.9 41.4 + - + -
138A ILE 2.7 26.1 + - - -
140A GLY 3.5 14.0 + - - -
141A GLU* 4.0 12.7 - - - +
142A GLY 3.2 27.8 + - - +
143A ALA* 4.9 6.3 - - - +
144A SER* 4.2 4.9 - - - +
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Residues in contact with VAL 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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60A VAL* 3.7 10.8 - - + -
62A PHE* 3.9 28.7 - - + -
101A ILE* 4.1 29.4 - - + +
104A LEU* 3.8 30.7 - - + -
105A GLN* 4.6 1.1 - - + -
109A TRP 3.8 5.6 - - - +
110A ARG* 1.3 78.8 - - - +
112A LEU* 1.3 62.7 + - - +
113A ILE* 4.2 8.5 - - + -
137A TRP* 3.5 3.6 - - - -
144A SER* 3.0 44.3 + - - +
145A ALA 3.0 5.5 + - - +
155A LEU* 4.3 1.4 - - + +
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Residues in contact with LEU 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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60A VAL 3.0 10.5 + - - +
61A ILE* 3.3 12.6 - - + +
62A PHE 2.9 25.8 + - - -
111A VAL* 1.3 74.7 - - - +
113A ILE* 1.3 68.7 + - - +
114A VAL* 4.1 14.4 - - + -
134A LEU* 3.8 29.2 - - + -
137A TRP* 3.5 38.6 - - + -
145A ALA* 3.3 26.0 - - + +
146A GLN 4.0 1.6 - - - +
147A ILE* 4.2 9.6 - - + -
152A ILE* 3.9 21.8 - - + -
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Residues in contact with ILE 113 (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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62A PHE* 3.6 34.5 - - + +
64A HIS* 3.6 40.2 - - + +
101A ILE* 3.9 26.0 - - + -
111A VAL* 4.2 4.9 - - + -
112A LEU* 1.3 75.9 - - - +
114A VAL* 1.3 58.8 + - - +
115A TRP* 3.7 24.1 + - + +
145A ALA 2.9 12.2 + - - +
146A GLN* 3.0 15.5 - - + +
147A ILE* 2.8 31.2 + - - +
155A LEU* 4.6 9.0 - - + -
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Residues in contact with VAL 114 (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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28A LEU* 4.5 11.4 - - + -
61A ILE* 3.8 23.8 - - + -
62A PHE 2.7 12.9 + - - +
63A THR* 3.3 11.2 - - + -
64A HIS 2.8 23.9 + - - -
112A LEU* 4.1 14.8 - - + -
113A ILE* 1.3 76.5 - - - +
115A TRP* 1.3 64.2 + - - +
116A GLU 3.7 0.2 + - - -
118A ALA* 4.9 3.4 - - + -
119A LEU* 3.6 37.1 - - + +
130A LEU* 5.1 3.1 - - + -
134A LEU* 4.6 1.6 - - + -
147A ILE* 3.9 22.4 - - + +
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Residues in contact with TRP 115 (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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64A HIS* 3.5 47.3 - + + +
65A GLY 4.4 1.8 - - - -
66A CYS* 4.1 2.7 - - - -
69A HIS* 3.7 24.5 - - + -
70A HIS 4.6 1.1 - - - -
71A HIS* 3.4 71.1 + + + +
97A ASP* 5.6 0.2 - - - -
113A ILE* 3.7 15.7 - - + +
114A VAL* 1.3 74.2 - - - +
116A GLU* 1.3 66.5 + - - +
117A CYS* 3.3 5.6 - - - -
118A ALA* 3.1 18.0 + - - +
119A LEU* 3.6 6.8 + - - +
146A GLN* 2.9 33.9 + - + -
147A ILE 3.1 23.6 + - - +
148A ASP* 4.5 3.1 - - + -
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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