Contacts of the strand formed by residues 174 - 179 (chain I) in PDB entry 5G04
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 ASN 174 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I ARG* 3.0 41.5 - - + +
115I TRP* 3.4 16.6 + - - +
116I MET 3.1 17.7 - - - +
117I GLU* 4.2 6.7 - - + +
168I LEU 5.3 0.4 + - - -
171I VAL* 4.3 6.6 - - - +
172I ARG 3.9 7.9 - - - +
173I LEU* 1.3 78.6 - - - +
175I ILE* 1.3 61.1 + - - +
189I ALA* 3.6 1.0 - - - -
190I TYR* 2.7 63.0 + - - +
191I GLY 4.4 0.2 + - - -
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Residues in contact with ILE 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I TRP* 3.3 8.5 - - - -
116I MET* 3.1 39.4 + - + +
173I LEU* 4.7 16.6 - - + +
174I ASN* 1.3 75.0 - - - +
176I LEU* 1.3 73.4 + - - +
177I VAL* 3.9 17.5 - - + +
187I LEU* 3.7 29.8 - - + -
188I TYR 3.6 6.7 - - - +
189I ALA* 5.0 1.1 - - - -
195I ILE* 5.0 11.2 - - + -
210I LEU* 3.7 10.5 - - + -
214I LEU* 3.7 34.1 - - + -
241I LEU* 3.9 17.9 - - + -
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Residues in contact with LEU 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ALA* 4.5 1.1 - - + -
81I ALA* 4.3 11.0 - - + -
92I LEU* 4.8 0.9 - - + -
104I PHE* 4.5 14.1 - - + -
113I MET* 4.0 25.4 - - + -
114I HIS 3.5 16.6 - - - +
115I TRP* 3.4 45.3 - - + +
175I ILE* 1.3 76.3 - - - +
177I VAL* 1.3 68.3 + - - +
178I LEU* 3.6 12.5 + - + +
188I TYR* 2.7 35.5 + - + +
191I GLY* 3.9 18.8 - - - -
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Residues in contact with VAL 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I MET* 3.2 5.9 - - - +
114I HIS* 2.9 43.3 + - + +
116I MET* 5.0 1.1 - - - -
175I ILE* 3.9 10.1 - - + -
176I LEU* 1.3 70.6 - - - +
178I LEU* 1.3 65.4 + - - +
185I ILE* 3.5 21.3 - - + -
186I GLU 3.8 3.6 - - - -
187I LEU* 4.1 11.0 - - + +
208I LEU* 3.4 30.5 - - + +
210I LEU* 3.7 38.8 - - + -
217I LEU* 4.4 8.5 - - + -
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Residues in contact with LEU 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I ILE* 3.1 29.6 - - + -
104I PHE* 4.3 3.8 - - + -
106I VAL* 4.5 3.8 - - + -
110I VAL* 3.9 10.5 - - + -
112I CYS 3.6 1.3 - - - -
113I MET* 3.5 41.7 - - + -
176I LEU* 3.7 12.1 - - + +
177I VAL* 1.3 84.2 - - - +
179I GLY* 1.3 58.5 + - - +
184I PHE 4.3 0.3 - - - +
185I ILE* 3.1 9.0 - - - +
186I GLU* 2.8 39.9 + - + +
188I TYR* 3.6 31.9 - - + -
208I LEU* 3.8 4.5 - - - -
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Residues in contact with GLY 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I PRO 5.1 0.2 - - - -
110I VAL* 3.2 8.6 - - - +
111I SER* 2.7 28.2 + - - -
112I CYS* 2.9 22.4 + - - -
178I LEU* 1.3 76.9 - - - +
180I GLY* 1.3 50.9 + - - -
182I SER* 5.5 0.2 - - - -
184I PHE 4.4 6.7 - - - -
185I ILE* 4.8 2.9 - - - -
205I CYS* 4.6 3.1 - - - -
208I LEU* 3.8 14.5 - - - +
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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