Contacts of the strand formed by residues 118 - 123 (chain C) in PDB entry 3GXM
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 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C LYS* 4.1 8.5 - - + -
80C GLY* 3.5 30.5 - - - +
81C PHE 3.2 8.1 + - - +
82C GLY* 3.0 22.5 - - - -
83C GLY 3.3 3.2 + - - -
109C PHE* 4.5 0.9 - - - -
116C TYR* 3.7 3.5 - - - -
117C ASN* 1.3 96.3 - - - +
119C ILE* 1.3 72.9 + - - +
172C VAL* 4.0 0.2 - - - -
173C SER* 3.2 22.0 - - - +
175C LEU* 4.7 9.2 - - + -
228C TRP* 4.8 5.2 - - + -
337C PHE* 3.6 33.2 - - + -
378C TRP 4.0 1.6 - - - +
379C THR* 3.4 21.1 - - - +
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Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C GLY 3.3 10.1 - - - +
85C MET* 3.6 33.2 - - + -
109C PHE* 3.6 33.7 - - + -
118C ILE* 1.3 81.6 - - - +
120C ARG* 1.3 66.0 + - - +
121C VAL* 3.9 8.1 + - + +
161C ILE* 4.3 13.0 - - + -
164C ALA* 3.9 17.5 - - + -
165C LEU* 3.9 8.5 - - + -
172C VAL* 3.9 16.0 - - + +
173C SER 3.1 7.1 + - - +
174C LEU* 3.4 15.1 - - + -
175C LEU* 2.8 25.5 + - - +
383C LEU* 4.7 2.9 - - + -
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Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C GLY 3.0 6.9 + - - -
84C ALA* 3.2 11.6 - - + +
85C MET 2.8 31.0 + - - -
119C ILE* 1.3 74.7 - - - +
121C VAL* 1.3 60.4 + - - +
122C PRO* 3.6 2.7 - - - +
175C LEU* 3.2 29.8 - - + +
177C SER* 3.1 20.5 + - - +
179C TRP* 3.6 16.2 - - - -
234C ASN* 2.8 24.9 + - - -
282C ASP* 2.8 27.9 + - - -
311C HIS* 3.8 1.0 + - - -
339C SER* 3.3 20.1 + - - -
340C GLU* 3.0 32.5 + - - +
379C THR* 3.4 24.0 + - + +
381C TRP* 3.8 9.0 - - - -
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C MET* 4.6 1.8 - - + +
119C ILE* 4.1 15.7 - - + +
120C ARG* 1.3 78.1 - - - +
122C PRO* 1.4 70.6 - - - +
123C MET* 3.6 0.3 + - - +
157C LYS* 3.7 17.9 - - - -
161C ILE* 3.9 22.9 - - + -
174C LEU* 4.6 6.1 - - + -
175C LEU 2.6 10.6 + - - +
176C ALA* 3.2 24.3 - - - +
177C SER 3.5 1.5 + - - -
216C PHE* 4.7 1.7 - - + -
220C TYR* 3.6 32.5 - - + +
227C PHE* 3.9 24.0 - - + -
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Residues in contact with PRO 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ALA* 4.9 3.4 - - + -
85C MET 3.7 13.5 - - - +
86C THR* 4.0 30.1 - - + -
87C ASP* 5.1 2.0 - - - +
120C ARG* 3.6 11.2 - - + +
121C VAL* 1.4 88.8 - - + +
123C MET* 1.3 59.7 + - - +
124C ALA 3.5 14.4 + - - +
126C CYS* 4.6 8.7 - - - -
135C TYR* 3.9 1.4 + - - -
157C LYS* 2.8 30.9 + - - +
177C SER 3.4 8.7 - - - +
179C TRP* 3.7 25.3 - - + -
216C PHE* 4.8 0.5 - - - -
381C TRP* 5.4 0.2 - - + -
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Residues in contact with MET 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C PRO* 1.3 70.0 - - - +
124C ALA* 1.3 70.8 + - - +
125C SER 4.7 0.7 - - - +
135C TYR* 3.7 14.6 - - + -
176C ALA* 4.0 24.9 - - + +
177C SER 2.9 15.9 + - - +
178C PRO* 3.3 43.4 - - + +
179C TRP* 4.2 6.6 + - - -
180C THR 4.8 4.5 + - - +
212C TYR* 4.2 19.2 + - + -
213C PHE* 4.0 31.0 - - + -
216C PHE* 3.6 38.6 - - + -
230C VAL* 5.2 1.6 - - + -
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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