Contacts of the strand formed by residues 144 - 148 (chain A) in PDB entry 3GYQ
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 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 4.1 14.8 - - - -
118A VAL* 3.5 4.2 - - - +
119A VAL* 3.0 25.5 + - - +
142A ALA* 3.3 2.9 - - - +
143A SER* 1.3 83.7 + - - +
145A ILE* 1.3 66.7 + - - +
171A LEU* 4.3 10.1 - - - -
172A PRO* 3.3 12.8 - - - -
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Residues in contact with ILE 145 (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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111A ILE* 4.2 0.9 - - - +
119A VAL* 3.2 20.0 - - + +
121A LEU* 4.5 5.4 - - + -
130A ILE* 6.5 0.2 - - + -
133A ILE* 3.8 17.3 - - + +
134A VAL* 3.8 22.4 - - + -
137A SER* 3.3 35.9 - - - +
144A GLY* 1.3 78.8 - - - +
146A ILE* 1.3 62.5 + - - +
147A LEU* 3.7 28.9 + - + -
171A LEU* 4.4 7.6 - - + -
172A PRO 2.9 9.4 + - - +
173A VAL* 3.5 9.7 - - + -
174A VAL* 2.8 33.3 + - - +
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Residues in contact with ILE 146 (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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108A PHE* 3.5 27.1 - - + -
111A ILE* 4.0 14.4 - - + -
118A VAL* 4.2 11.2 - - + -
119A VAL 2.7 10.4 + - - +
120A VAL* 3.6 26.9 - - + +
121A LEU* 2.9 28.4 + - - +
145A ILE* 1.3 75.8 - - - +
147A LEU* 1.3 60.7 + - - +
148A VAL* 3.4 24.0 + - + -
174A VAL* 3.4 9.2 - - + +
176A SER* 4.1 10.8 - - - -
181A ALA* 3.9 15.7 - - + -
184A PHE* 4.2 13.5 - - + -
185A ILE* 5.0 4.5 - - + -
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Residues in contact with LEU 147 (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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121A LEU* 3.6 34.5 - - + -
124A VAL 5.7 0.4 - - - +
130A ILE* 3.9 32.3 - - + -
145A ILE* 3.7 13.0 - - + -
146A ILE* 1.3 69.0 - - - +
148A VAL* 1.3 62.6 + - - +
149A ASP 3.8 1.4 + - - -
150A SER* 3.8 22.0 + - - +
152A ILE* 5.3 0.9 - - + -
160A LEU* 4.7 9.0 - - + -
173A VAL* 3.6 31.0 - - + -
174A VAL 2.7 10.9 + - - +
175A LEU* 3.6 22.9 - - + +
176A SER 3.3 20.2 + - - +
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Residues in contact with VAL 148 (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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120A VAL* 4.5 6.1 - - + -
121A LEU 2.9 20.6 + - - +
122A ASP* 3.8 18.4 - - + +
123A GLY 2.9 21.5 + - - -
124A VAL 4.4 0.7 + - - -
146A ILE* 3.9 13.5 - - + +
147A LEU* 1.3 70.1 - - - +
149A ASP* 1.3 75.3 + - + +
150A SER* 4.4 1.0 - - - -
176A SER 3.4 12.6 - - - +
177A GLY* 4.0 2.0 - - - +
178A ARG* 3.8 33.7 - - + +
181A ALA* 3.9 28.3 - - + -
228A PHE* 4.6 3.8 - - + -
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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