Contacts of the strand formed by residues 159 - 165 (chain C) in PDB entry 1R4N
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 VAL 159 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ARG 3.8 0.9 - - - +
155C THR* 3.8 2.9 - - - -
156C TYR* 2.7 38.2 + - + +
157C GLY 3.3 0.4 - - - -
158C LEU* 1.3 82.5 - - - +
160C GLY* 1.3 69.4 + - - +
161C TYR* 3.8 2.1 + - + +
425C LEU* 3.9 39.3 - - + -
429C LEU* 4.7 18.8 - - + -
482C PHE* 3.8 24.7 - - + -
485C TYR* 4.1 11.0 - - + +
493C ILE* 4.2 4.2 - - - +
521C ILE* 4.6 5.2 - - + -
522C TYR 3.2 6.1 - - - +
523C SER* 5.2 0.7 - - - -
525C MET* 5.5 1.6 - - - -
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Residues in contact with GLY 160 (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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154C ARG 3.8 3.6 - - - -
158C LEU 4.1 0.4 + - - -
159C VAL* 1.3 74.7 - - - +
161C TYR* 1.3 58.5 + - - -
493C ILE* 4.6 3.8 - - - -
497C LEU* 3.8 23.3 - - - +
520C TYR* 3.6 1.7 - - - +
521C ILE* 3.4 7.3 - - - +
522C TYR* 2.6 52.1 + - - +
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Residues in contact with TYR 161 (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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152C ILE* 4.5 22.4 - - + +
153C CYS* 3.5 0.3 - - - -
154C ARG* 2.7 66.4 + - + +
159C VAL* 3.8 2.8 + - + +
160C GLY* 1.3 72.8 - - - +
162C MET* 1.3 71.8 + - - +
163C ARG* 3.5 28.2 - - + +
398C LEU* 5.2 2.8 - - - +
401C GLU* 4.8 1.7 + - - -
402C TYR* 4.9 7.6 + - - -
426C TYR* 4.1 22.5 + + - -
429C LEU* 3.5 33.4 - - + -
497C LEU* 3.5 3.1 - - - +
519C THR* 3.4 30.6 + - + -
520C TYR 3.8 2.5 - - - -
521C ILE* 4.4 8.1 - - + -
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Residues in contact with MET 162 (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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151C LEU* 4.1 11.7 - - + -
152C ILE 3.3 5.8 - - - -
153C CYS* 3.8 15.5 - - - -
161C TYR* 1.3 81.6 - - - +
163C ARG* 1.3 59.2 + - - +
497C LEU* 4.0 16.2 - - + +
500C ALA* 4.3 4.7 - - + -
501C ALA* 3.6 35.9 - - - +
504C GLU* 4.6 1.6 - - + -
516C PHE* 3.5 24.6 - - + -
519C THR* 4.5 0.7 - - - -
520C TYR* 2.8 51.3 + - + +
330D LEU* 3.3 34.5 - - + -
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Residues in contact with ARG 163 (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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150C LEU 4.2 0.2 - - - +
151C LEU* 3.5 4.0 - - - +
152C ILE* 2.8 44.1 + - + +
161C TYR* 3.5 21.6 - - + +
162C MET* 1.3 73.5 - - - +
164C ILE* 1.3 89.0 + - - +
165C ILE* 3.4 16.7 - - + +
395C CYS* 4.7 1.6 - - - +
396C ARG* 2.7 33.1 + - - +
397C SER 3.9 4.6 + - - -
398C LEU* 3.7 19.1 - - - +
401C GLU* 2.6 32.9 + - - +
518C ASN* 2.8 33.5 + - - +
519C THR* 3.4 23.6 - - - +
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Residues in contact with ILE 164 (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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150C LEU 3.7 8.7 - - - +
151C LEU* 3.7 8.5 - - + -
163C ARG* 1.3 98.9 + - - +
165C ILE* 1.3 62.4 + - - +
166C ILE* 4.0 11.9 - - + +
395C CYS* 3.8 11.7 - - - -
504C GLU* 5.3 2.7 - - + -
508C ILE* 3.8 25.1 - - + -
515C ILE* 3.6 35.2 - - + -
516C PHE* 3.4 48.1 - - + +
518C ASN* 3.9 10.7 - - - +
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Residues in contact with ILE 165 (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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140C ALA* 3.7 20.2 - - + +
144C TRP* 3.6 32.7 - - + -
148C ILE 4.0 4.3 - - - +
149C PRO* 3.8 2.8 - - - +
150C LEU* 2.8 49.5 + - + +
152C ILE* 4.4 7.0 - - + -
163C ARG* 3.4 18.2 - - + +
164C ILE* 1.3 83.4 - - - +
166C ILE* 1.3 59.9 + - - +
167C LYS 4.4 0.3 + - - -
395C CYS* 4.2 2.9 - - + -
396C ARG 4.7 1.1 - - - +
397C SER* 4.6 1.3 - - - -
398C LEU* 3.6 42.8 - - + +
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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