Contacts of the strand formed by residues 118 - 123 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LYS* 3.9 23.6 - - + +
80A GLY 4.0 11.0 - - - +
81A PHE 3.1 11.3 + - - +
82A GLY* 3.0 21.4 - - - -
83A GLY 3.4 2.9 + - - -
109A PHE* 4.7 0.7 - - - -
116A TYR* 3.7 4.0 - - - -
117A ASN* 1.3 99.8 + - - +
119A ILE* 1.3 75.7 + - - +
120A ARG 4.3 0.2 - - - -
173A SER* 3.4 13.5 - - - +
175A LEU* 4.8 4.7 - - + -
228A TRP* 4.4 11.4 - - + -
337A PHE* 3.8 32.1 - - + -
378A TRP 5.3 0.2 - - - +
379A THR* 3.3 22.9 - - - +
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Residues in contact with ILE 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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83A GLY 3.5 8.5 - - - +
85A MET* 3.9 24.5 - - + -
109A PHE* 3.7 21.8 - - + -
118A ILE* 1.3 81.6 - - - +
120A ARG* 1.3 74.8 + - - +
121A VAL* 3.9 8.5 + - + +
161A ILE* 4.3 16.4 - - + -
164A ALA* 3.7 30.5 - - + -
165A LEU* 4.0 17.9 - - + -
172A VAL* 4.0 5.1 - - + +
173A SER 3.1 7.5 + - - -
174A LEU* 3.5 11.7 - - + -
175A LEU* 2.8 25.6 + - - +
383A LEU* 5.0 1.6 - - + -
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Residues in contact with ARG 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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83A GLY 3.1 8.1 + - - -
84A ALA* 3.3 13.9 - - + +
85A MET 2.9 29.6 + - - -
118A ILE 4.3 0.6 - - - -
119A ILE* 1.3 73.0 - - - +
121A VAL* 1.3 67.0 + - - +
122A PRO* 3.9 1.8 - - + +
175A LEU* 3.2 23.1 - - + +
177A SER* 3.2 20.2 + - - +
179A TRP* 3.6 18.7 - - + -
234A ASN* 2.4 31.3 + - - -
282A ASP* 3.1 25.7 + - - -
311A HIS* 3.8 1.0 + - - -
339A SER* 3.4 21.7 + - - -
340A GLU* 3.2 31.9 + - - +
379A THR* 3.6 20.1 + - + +
381A TRP* 3.7 10.5 - - - -
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Residues in contact with VAL 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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85A MET* 4.6 2.2 - - + +
119A ILE* 4.0 12.1 - - + +
120A ARG* 1.3 80.1 - - - +
122A PRO* 1.3 78.3 - - - +
157A LYS* 3.9 10.3 - - - -
161A ILE* 4.0 22.4 - - + -
174A LEU* 4.7 5.4 - - + -
175A LEU 2.6 11.1 + - - +
176A ALA* 3.2 4.0 - - - +
177A SER 3.1 21.2 + - - -
216A PHE* 4.4 2.5 - - + -
220A TYR* 3.9 23.6 - - + +
227A PHE* 3.7 34.1 - - + -
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Residues in contact with PRO 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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84A ALA* 5.2 0.9 - - + -
85A MET 3.3 22.2 - - - +
86A THR* 3.9 27.1 - - + -
87A ASP 5.3 0.4 - - - +
120A ARG* 3.9 6.1 - - + +
121A VAL* 1.3 90.5 - - + +
123A MET* 1.3 59.5 + - - +
124A ALA 3.6 14.8 - - - +
126A CYS* 4.3 9.9 - - - -
135A TYR* 3.8 1.6 + - - -
157A LYS* 3.0 25.7 + - - +
177A SER 3.4 6.5 - - - +
179A TRP* 3.6 27.8 - - + -
216A PHE* 4.4 0.3 - - - -
381A TRP* 4.8 1.3 - - + -
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Residues in contact with MET 123 (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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122A PRO* 1.3 69.6 - - - +
124A ALA* 1.3 69.8 + - - +
125A SER 4.7 1.2 - - - +
135A TYR* 3.5 14.6 - - + -
176A ALA* 3.8 23.6 - - + -
177A SER 2.9 21.5 + - - +
178A PRO* 3.4 43.6 - - + +
179A TRP* 4.3 5.2 + - - -
180A THR 4.7 4.7 + - - +
212A TYR* 4.3 17.3 + - + -
213A PHE* 4.0 34.5 - - + -
216A PHE* 3.8 36.6 - - + -
230A VAL* 5.4 0.4 - - - -
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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