Contacts of the strand formed by residues 140 - 145 (chain B) in PDB entry 1GXD
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 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TRP* 4.3 7.6 - - + +
95B ILE* 3.9 22.9 - - + -
96B THR 2.8 4.3 + - - +
97B TYR* 2.8 40.1 - - + +
98B ARG 2.9 5.9 + - - -
119B PHE* 3.9 16.8 - - + -
138B ALA* 4.3 0.4 - - - -
139B ASP* 1.3 80.4 - - + +
141B MET* 1.3 61.2 + - - +
142B ILE* 3.7 7.5 + - + -
174B GLY 3.1 22.2 - - - +
175B ASP* 4.2 1.8 - - - -
176B SER* 3.6 13.5 - - - +
376B PHE* 4.7 1.6 - - + -
379B ALA* 3.8 11.2 - - + -
380B MET* 3.6 33.0 - - + -
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Residues in contact with MET 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ARG* 3.7 12.1 - - - +
100B ILE* 3.1 38.4 - - + -
136B GLY 4.5 6.5 - - - +
137B GLU* 3.2 28.9 - - + +
138B ALA* 3.6 36.3 - - - +
140B ILE* 1.3 74.1 - - - +
142B ILE* 1.3 61.2 + - - +
143B ASN* 4.0 1.5 + - + +
175B ASP* 3.1 32.4 + - - +
176B SER 3.1 21.5 + - - +
177B HIS* 4.6 1.9 + - - -
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 3.6 24.9 - - + -
98B ARG 2.6 18.3 + - - +
99B ILE* 3.5 5.6 - - + -
100B ILE* 2.7 34.4 + - - +
101B GLY 3.6 1.5 + - - +
115B PHE* 3.4 42.2 - - + -
119B PHE* 4.5 0.7 - - + -
140B ILE* 4.1 12.1 - - + +
141B MET* 1.3 74.1 - - - +
143B ASN* 1.3 63.0 + - - +
144B PHE* 5.1 0.4 - - + -
176B SER* 3.4 5.2 - - - +
178B PHE* 3.4 20.2 - - + -
376B PHE* 3.3 33.4 - - + -
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Residues in contact with ASN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ILE* 4.1 19.6 + - + +
101B GLY* 3.4 25.7 - - - +
141B MET 4.0 1.7 + - - +
142B ILE* 1.3 75.8 - - - +
144B PHE* 1.3 105.8 + - - +
176B SER 3.2 6.6 + - - +
177B HIS* 3.3 19.3 - - + +
178B PHE* 3.0 25.5 + - - -
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A GLN* 4.6 2.8 - - - +
101B GLY 3.2 31.6 - - - -
102B TYR* 3.6 16.8 - - - +
103B THR* 4.0 26.0 - - + -
111B VAL* 4.5 2.5 - - + -
115B PHE* 3.8 31.6 - + - -
142B ILE* 5.1 0.2 - - + -
143B ASN* 1.3 110.3 + - - +
145B GLY* 1.3 60.6 + - - +
149B HIS* 5.2 2.6 - - - +
177B HIS* 5.8 1.6 - - - -
178B PHE* 3.2 30.3 - + + +
179B ASP 4.8 0.2 - - - -
180B ASP* 4.3 15.5 - - + +
184B TRP* 4.0 19.1 - + - -
368B LEU* 3.9 20.4 - - + -
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A GLN* 4.0 7.0 - - - -
144B PHE* 1.3 77.5 - - - +
146B ARG* 1.3 62.2 + - - -
149B HIS* 3.9 16.6 - - - -
155B PHE* 3.2 19.0 - - - -
178B PHE 2.8 11.7 + - - -
179B ASP* 3.3 0.5 - - - +
180B ASP* 2.8 30.9 + - - +
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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