Contacts of the strand formed by residues 172 - 180 (chain C) in PDB entry 3L9J
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 172 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C THR* 3.6 6.7 - - - -
68C LYS 2.8 27.9 + - - +
109C GLU* 4.0 36.8 - - + +
111C TRP* 3.6 37.4 + - + +
154C VAL* 3.2 29.4 - - + -
166C LYS* 3.9 15.7 - - + +
170C ASP* 3.9 6.3 + - + +
171C GLN* 1.3 80.8 - - - +
173C PRO* 1.3 77.1 - - + +
174C TYR* 3.6 3.8 - - - -
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Residues in contact with PRO 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE 3.1 18.6 - - - +
65C THR* 3.9 16.4 - - - +
67C THR* 3.8 15.7 - - + -
104C VAL* 3.9 24.0 - - + -
108C ALA* 5.0 1.6 - - + -
109C GLU 3.1 28.5 - - - +
110C ILE* 3.3 8.3 - - + -
111C TRP* 3.2 19.1 + - - -
172C LEU* 1.3 91.8 - - + +
174C TYR* 1.3 64.0 + - + +
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Residues in contact with TYR 174 (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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63C ALA* 4.2 0.3 - - - +
64C PHE* 2.8 59.4 + + + +
66C GLN 3.8 11.5 + - - -
68C LYS* 3.7 31.4 - - + +
73C ALA* 3.5 35.0 - - + -
76C ASP* 2.3 36.2 + - + +
77C CYS* 4.1 4.7 - - - -
84C LEU* 3.7 16.2 - - + -
104C VAL* 5.1 0.3 - - - +
110C ILE* 3.9 12.1 - - - +
111C TRP* 4.0 9.6 - - + +
172C LEU 3.6 7.0 - - - -
173C PRO* 1.3 79.5 - - + +
175C ILE* 1.3 66.5 + - - +
176C CYS* 4.0 16.2 - - - -
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Residues in contact with ILE 175 (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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61C PHE* 3.9 11.2 - - + -
62C LEU 3.4 9.6 - - - +
63C ALA* 3.9 14.1 - - + -
77C CYS* 4.5 0.9 - - - -
84C LEU* 3.9 7.9 - - - +
85C SER* 3.5 22.2 + - - -
96C LEU* 3.8 23.3 - - + -
99C TYR* 3.8 30.3 - - + -
100C LEU* 3.9 22.4 - - + -
103C SER* 4.4 1.6 - - - +
104C VAL* 4.8 0.2 - - + -
110C ILE* 3.6 35.4 - - + +
111C TRP 4.7 1.7 + - - +
174C TYR* 1.3 81.9 - - - +
176C CYS* 1.3 73.9 + - - +
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Residues in contact with CYS 176 (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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61C PHE* 3.3 5.4 - - - -
62C LEU 2.8 34.0 + - - -
64C PHE* 3.5 28.3 - - + -
76C ASP 4.7 0.9 - - - -
77C CYS* 2.0 56.8 - - + -
80C ARG* 4.8 0.2 - - - -
83C THR 3.5 3.8 - - - -
174C TYR* 4.0 5.4 - - - -
175C ILE* 1.3 75.5 - - - +
177C GLN* 1.3 60.7 + - - +
178C PHE* 3.6 25.0 - - + -
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Residues in contact with GLN 177 (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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59C LYS* 3.5 26.8 - - + +
60C CYS 3.4 5.8 - - - +
61C PHE* 3.7 22.9 - - + -
82C GLY* 3.1 5.4 - - - -
83C THR* 2.8 51.3 + - + +
85C SER* 2.7 35.6 + - - +
86C THR 4.3 4.7 + - - +
92C GLU* 5.9 0.8 + - - -
175C ILE 4.0 0.4 + - - -
176C CYS* 1.3 74.1 - - - +
178C PHE* 1.3 66.9 + - - +
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Residues in contact with PHE 178 (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* 5.8 2.5 - - + -
59C LYS* 3.3 7.8 - - - +
60C CYS* 2.9 48.8 + - + +
62C LEU* 3.9 24.9 - - + -
77C CYS 4.6 0.2 - - - -
80C ARG* 3.3 42.8 - - + -
81C GLY 3.9 4.0 - - - +
82C GLY* 3.7 25.4 - - - -
176C CYS* 3.6 37.5 - - + -
177C GLN* 1.3 78.9 - - - +
179C GLY* 1.3 59.7 + - - +
180C ILE* 4.1 10.2 + - + -
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Residues in contact with GLY 179 (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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58C MET 3.5 5.4 - - - -
59C LYS* 4.8 0.9 - - - -
81C GLY 5.3 2.6 + - - -
178C PHE* 1.3 73.4 - - - +
180C ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 180 (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* 6.4 0.2 - - + -
50C CYS* 4.9 1.1 - - - -
57C HIS* 3.2 34.3 + - - -
58C MET* 2.7 37.3 + - + +
60C CYS* 3.6 31.9 - - + -
178C PHE* 4.7 7.0 - - + +
179C GLY* 1.3 81.1 - - - +
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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