Contacts of the strand formed by residues 256 - 262 (chain C) in PDB entry 4GXU
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 TYR 256 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C LYS* 4.1 25.8 - - + -
121C PHE* 3.2 24.2 - - - +
122C GLU* 3.5 31.8 + - + -
123C ILE* 4.1 2.5 - - - +
149C ARG* 3.5 21.3 - - + -
150C ASN* 3.1 35.0 + - - +
151C LEU* 5.6 0.2 - - - +
179C LEU* 5.3 8.3 + - - +
254C PRO* 5.1 2.6 - - - +
255C TRP* 1.3 113.3 + + - +
257C ALA* 1.3 62.8 + - - +
258C PHE* 4.7 3.8 - - - -
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Residues in contact with ALA 257 (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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120C LYS* 3.4 5.9 - - - +
121C PHE* 2.9 42.2 + - + -
123C ILE* 4.1 16.9 - - + +
176C VAL* 3.9 15.7 - - + -
177C LEU 3.2 17.5 - - - +
178C VAL* 4.4 7.6 - - + +
179C LEU* 5.7 0.4 - - - +
254C PRO* 5.9 0.4 - - + -
256C TYR* 1.3 74.4 - - - +
258C PHE* 1.3 70.9 + - - +
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Residues in contact with PHE 258 (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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69C TRP* 5.0 7.0 - - - -
70C LEU* 3.8 33.0 - - + -
118C PHE* 3.3 37.7 - + + -
119C GLU 3.6 3.6 - - - -
120C LYS* 3.4 27.8 - - + -
121C PHE* 4.2 0.9 - - - -
150C ASN* 3.7 24.0 - - - -
176C VAL* 4.2 1.6 - - - -
177C LEU* 2.6 49.3 + - + +
179C LEU* 3.9 21.3 - - + -
256C TYR 4.7 3.6 - - - -
257C ALA* 1.3 88.5 - - - +
259C ALA* 1.3 59.5 + - - +
260C LEU* 3.5 12.6 + - + +
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Residues in contact with ALA 259 (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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118C PHE* 3.0 26.1 - - - -
119C GLU* 3.1 33.5 + - + +
121C PHE* 4.0 3.5 - - + -
172C LYS* 3.9 12.3 - - + -
174C LYS* 3.5 23.5 - - + +
175C GLU 3.1 6.7 - - - +
176C VAL* 3.7 15.7 - - + -
258C PHE* 1.3 70.7 - - - +
260C LEU* 1.3 59.5 + - - +
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Residues in contact with LEU 260 (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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108C LEU* 6.2 0.2 - - + -
112C LEU* 4.5 13.9 - - + -
115C VAL* 3.8 19.7 - - + -
117C SER 4.1 1.1 - - - -
118C PHE* 3.6 22.4 - - + -
174C LYS* 3.6 17.9 - - - +
175C GLU* 2.5 31.3 + - + +
177C LEU* 3.8 16.2 - - + -
236C LEU* 3.6 30.7 - - + -
258C PHE* 3.7 20.6 - - + +
259C ALA* 1.3 74.1 - - - +
261C ASN* 1.3 64.4 + - - +
262C ARG* 3.9 20.6 + - - +
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Residues in contact with ASN 261 (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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114C SER 2.9 12.3 - - - +
115C VAL* 3.1 3.4 - - - -
116C SER* 3.0 36.5 + - - +
117C SER* 2.2 47.7 + - - +
119C GLU* 4.3 0.6 + - - -
174C LYS* 3.6 37.7 + - - +
260C LEU* 1.3 74.2 - - - +
262C ARG* 1.3 60.9 + - - +
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Residues in contact with ARG 262 (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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108C LEU* 5.7 1.2 - - - +
111C GLN* 2.5 46.8 + - - +
112C LEU* 5.5 1.2 - - - +
114C SER* 2.3 42.9 + - - -
115C VAL* 5.6 1.3 - - - -
116C SER* 4.9 5.6 + - - -
175C GLU* 2.9 31.1 + - - +
234C TRP* 5.7 0.6 - - - -
236C LEU* 3.0 39.5 - - - +
260C LEU* 3.9 16.9 - - - +
261C ASN* 1.3 73.4 - - - +
263C GLY* 1.3 57.3 + - - +
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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