Contacts of the strand formed by residues 117 - 122 (chain A) in PDB entry 5CLQ
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 ILE 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ALA* 3.3 13.9 - - + +
88A ILE* 3.9 31.9 - - + -
105A HIS* 3.7 24.0 - - + +
108A LEU* 4.8 7.9 - - + -
109A VAL* 3.7 19.3 - - + -
115A ILE* 3.3 37.2 - - + +
116A PRO* 1.3 76.6 - - - +
118A VAL* 1.3 71.3 + - - +
138A PHE* 4.4 9.0 - - + -
143A ASN 3.0 7.9 + - - -
144A LEU* 3.4 13.7 - - + +
145A GLN 3.1 22.9 + - - -
163A TRP* 4.0 1.3 - - - -
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Residues in contact with VAL 118 (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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86A ALA 3.0 8.0 + - - +
87A ILE* 3.4 10.0 - - + +
88A ILE* 2.7 33.3 + - - +
117A ILE* 1.3 78.2 - - - +
119A LEU* 1.3 67.4 + - - +
120A CYS* 3.9 12.8 - - - -
138A PHE* 4.8 0.2 - - - -
145A GLN 3.2 11.4 - - - +
147A TYR* 3.8 23.1 - - + -
160A PRO* 4.0 9.0 - - + +
163A TRP* 3.5 31.0 - - + -
164A LEU* 3.7 24.9 - - + -
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Residues in contact with LEU 119 (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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88A ILE* 3.2 22.9 - - + +
90A PHE* 3.5 35.7 - - + -
98A TYR* 4.5 8.5 - - + -
101A VAL* 3.7 26.7 - - + -
117A ILE 4.2 0.2 - - - -
118A VAL* 1.3 76.7 - - - +
120A CYS* 1.3 60.1 + - - +
136A ILE* 4.6 3.4 - - + -
138A PHE* 3.4 44.1 - - + -
145A GLN 2.7 10.3 + - - +
146A TYR* 3.1 20.7 - - + -
147A TYR 3.0 26.3 + - - -
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Residues in contact with CYS 120 (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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26A PHE* 5.7 0.9 - - - -
87A ILE* 3.8 20.2 - - + -
88A ILE 2.9 10.7 + - - +
89A MET* 3.6 9.8 - - - -
90A PHE* 2.9 31.2 + - - +
118A VAL* 3.9 6.1 - - - -
119A LEU* 1.3 78.3 - - - +
121A GLY* 1.3 59.8 + - - +
122A ASN 3.5 0.3 + - - -
146A TYR* 4.1 2.7 - - - -
147A TYR* 3.3 4.3 - - - -
149A ILE* 3.6 30.5 - - + -
160A PRO* 3.5 32.1 - - - -
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Residues in contact with GLY 121 (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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90A PHE* 3.5 13.0 - - - -
92A VAL* 3.7 10.9 - - - +
120A CYS* 1.3 69.6 - - - +
122A ASN* 1.3 68.7 + - - +
124A VAL* 3.2 15.6 - - - +
146A TYR* 3.5 18.3 - - - -
147A TYR 3.1 11.3 + - - -
148A ASP* 4.0 0.3 - - - -
149A ILE 3.1 16.6 + - - +
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Residues in contact with ASN 122 (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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21A THR 2.7 29.3 + - - +
22A GLY* 3.5 12.3 + - - -
26A PHE* 5.8 0.7 - - - -
89A MET* 3.7 20.4 - - - -
90A PHE 2.9 9.9 + - - +
92A VAL* 3.2 17.7 + - - +
120A CYS 3.5 2.6 + - - -
121A GLY* 1.3 80.1 - - - +
123A LYS* 1.3 87.0 + - + +
149A ILE* 3.4 12.9 - - + +
150A SER* 3.5 2.6 + - - -
151A ALA* 3.1 26.1 + - - +
301A GNP 3.0 25.0 + - - +
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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