Contacts of the strand formed by residues 157 - 163 (chain C) in PDB entry 3GZN
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 LEU 157 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C VAL* 5.1 1.3 - - - -
133C VAL* 3.4 12.1 - - + +
135C ALA* 4.2 8.1 - - + -
143C SER 5.2 0.2 - - - +
146C LEU* 3.8 23.8 - - + -
147C ALA* 3.5 37.7 - - + +
150C LEU* 4.0 20.6 - - + -
155C ILE 3.3 4.3 + - - +
156C PRO* 1.3 73.9 - - - +
158C LEU* 1.3 77.2 + - - +
159C ILE* 4.1 12.1 - - + -
170C ARG 4.1 0.4 - - - +
171C ILE* 3.9 4.5 - - - +
172C ILE* 3.0 57.9 + - + +
173C ILE* 5.3 0.3 - - - +
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Residues in contact with LEU 158 (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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132C VAL* 4.9 4.5 - - + -
133C VAL 2.8 12.8 + - - +
134C VAL* 3.4 11.3 - - + +
135C ALA 2.9 28.2 + - - +
157C LEU* 1.3 74.9 - - - +
159C ILE* 1.3 63.3 + - - +
160C CYS* 4.0 16.8 - - - -
169C MET* 4.5 6.1 - - + -
170C ARG 3.4 17.7 - - - +
171C ILE* 3.7 30.3 - - + +
508C ALA* 3.8 15.7 - - + +
511C GLU* 4.5 7.4 - - + -
512C VAL* 3.4 31.4 - - + +
515C ILE* 5.3 1.6 - - + -
523C PHE* 4.1 12.3 - - + -
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Residues in contact with ILE 159 (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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135C ALA* 3.4 13.7 - - + +
136C THR* 5.8 0.2 - - - -
138C LEU* 5.5 8.5 - - + +
143C SER* 3.3 29.8 - - - +
146C LEU* 6.0 0.4 - - + -
157C LEU* 4.1 22.2 - - + -
158C LEU* 1.3 74.8 - - - +
160C CYS* 1.3 66.0 + - - +
161C ARG* 5.8 4.0 - - + -
168C TYR* 4.3 16.0 - - + +
169C MET* 3.0 7.4 - - - +
170C ARG* 2.8 46.8 + - + +
172C ILE* 4.1 14.8 - - + -
405C LEU* 4.0 23.6 - - + -
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Residues in contact with CYS 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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48C THR* 4.2 6.1 - - + -
52C ILE* 3.8 29.2 - - + -
134C VAL* 4.3 7.0 - - - -
135C ALA 2.8 10.3 + - - +
136C THR* 3.2 6.4 - - + -
137C GLN 3.1 23.2 + - - -
158C LEU* 4.0 17.5 - - - -
159C ILE* 1.3 85.3 - - - +
161C ARG* 1.3 62.3 + - - +
168C TYR* 3.4 4.7 - - - -
169C MET* 4.0 13.5 - - - -
504C LEU* 4.0 13.5 - - + -
508C ALA* 4.0 9.2 - - - -
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Residues in contact with ARG 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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48C THR* 4.8 0.2 - - - -
137C GLN* 3.4 19.0 + - - +
138C LEU 3.9 19.8 + - - +
139C PRO* 5.1 0.2 - - - +
159C ILE* 5.8 3.8 - - + -
160C CYS* 1.3 76.6 - - - +
162C THR* 1.3 69.6 + - - +
163C TYR* 4.1 12.5 + - + -
166C VAL 4.0 0.5 - - - +
167C GLY* 3.5 2.6 - - - -
168C TYR* 2.9 57.2 + - + +
436C LEU* 3.5 32.2 + - + +
439C VAL* 4.6 1.6 - - - +
440C ASP* 2.6 41.4 + - - -
449C TYR* 3.1 35.6 + - - -
504C LEU* 3.3 6.7 - - - +
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Residues in contact with THR 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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48C THR* 2.9 27.4 + - - +
137C GLN* 2.7 28.2 + - - +
161C ARG* 1.3 75.8 + - - +
163C TYR* 1.3 68.1 + - - +
164C GLY 3.8 5.6 - - - +
166C VAL 3.7 3.4 - - - -
494C ALA 5.4 0.9 - - - +
495C ALA 4.2 3.5 - - - +
496C GLU* 3.8 29.8 - - + -
497C PRO* 3.9 5.2 - - + +
500C ILE* 3.7 26.2 - - + +
501C ALA* 3.4 15.5 + - - +
504C LEU* 4.1 4.9 - - - +
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Residues in contact with TYR 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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137C GLN* 6.1 0.2 - - - -
161C ARG* 4.1 17.5 - - + -
162C THR* 1.3 77.8 - - - +
164C GLY* 1.3 67.2 + - - +
165C LEU 3.3 0.2 + - - -
166C VAL* 3.0 30.3 + - + +
436C LEU* 4.2 19.3 - - + -
439C VAL* 3.6 22.6 - - + +
449C TYR* 3.9 12.5 - + - +
450C PRO* 3.5 31.4 + - - +
489C PHE* 3.8 44.1 + + - -
492C TYR* 4.0 7.9 - + + -
494C ALA* 3.7 39.0 + - + -
495C ALA 3.8 2.9 - - - -
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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