Contacts of the strand formed by residues 143 - 148 (chain B) in PDB entry 2CUA
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 GLY 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B ARG 4.6 0.2 - - - -
142B PRO* 1.3 75.5 - - - +
144B GLU* 1.3 62.4 + - - -
145B TYR* 3.6 7.7 - - - -
165B VAL* 3.8 3.5 - - - -
166B VAL* 2.9 37.5 + - - +
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Residues in contact with GLU 144 (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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143B GLY* 1.3 71.8 - - - -
145B TYR* 1.3 69.2 + - - +
146B ARG 4.4 0.2 + - - -
163B THR* 3.8 30.2 + - + +
164B ILE 3.4 4.0 - - - +
165B VAL* 4.7 8.3 - - + +
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Residues in contact with TYR 145 (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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118B VAL* 3.8 26.5 - - + -
119B GLU 4.2 8.7 - - - +
120B GLY* 6.2 0.7 - - - -
121B THR* 4.2 13.7 - - + -
137B TYR* 5.6 1.1 - + - -
139B PHE* 3.7 21.7 - + - +
140B LYS 4.8 1.2 + - - -
141B ARG* 2.6 41.2 + - + +
143B GLY* 3.6 10.1 - - - -
144B GLU* 1.3 80.3 - - - +
146B ARG* 1.3 59.6 + - - +
163B THR* 3.5 7.1 - - - +
164B ILE* 2.7 42.3 + - + +
166B VAL* 3.4 33.7 - - + -
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Residues in contact with ARG 146 (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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117B HIS 3.5 1.0 - - - +
118B VAL* 3.3 3.4 - - - -
119B GLU* 2.7 64.6 + - + +
145B TYR* 1.3 73.8 - - - +
147B ILE* 1.3 61.9 + - - +
148B ILE* 3.3 31.7 - - + +
161B PHE* 5.0 8.7 - - + -
162B GLY 3.8 7.0 - - - +
163B THR* 5.0 0.2 - - - +
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Residues in contact with ILE 147 (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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90B TYR* 3.6 32.1 - - + +
92B PRO 5.7 0.7 - - - +
95B ILE* 4.0 13.5 - - + -
116B PHE* 3.8 32.5 - - + -
117B HIS 3.3 9.4 - - - +
118B VAL* 4.2 5.2 - - + -
146B ARG* 1.3 72.6 - - - +
148B ILE* 1.3 75.8 + - - +
161B PHE* 3.3 3.8 - - - -
162B GLY* 2.8 44.9 + - - +
163B THR 3.9 13.5 - - - +
164B ILE* 3.8 34.8 - - + -
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Residues in contact with ILE 148 (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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90B TYR* 3.3 9.5 + - - -
115B GLY 3.6 1.2 - - - +
117B HIS* 2.8 45.5 + - + +
119B GLU* 4.2 17.7 - - - +
146B ARG* 3.3 35.0 - - + +
147B ILE* 1.3 86.8 - - - +
149B CYS* 1.3 73.6 + - - +
150B ASN* 4.0 7.4 - - - +
160B MET 4.1 2.5 - - - +
161B PHE* 3.3 30.3 - - + -
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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