Contacts of the strand formed by residues 118 - 125 (chain C) in PDB entry 2P80
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 GLU 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A PRO* 4.2 7.6 - - - +
338A SER* 3.2 33.7 - - - +
339A GLY* 3.9 3.8 + - - +
86C ILE* 5.2 0.9 - - - -
87C ASN* 3.2 23.8 + - - +
114C ILE* 3.4 17.5 - - + +
115C ASN* 2.9 45.8 + - - +
116C PRO 4.3 2.5 - - - +
117C GLY* 1.3 85.7 - - - +
119C LYS* 1.3 60.3 + - - +
106D LYS* 4.8 10.0 + - - -
108D PRO* 6.3 1.8 - - + -
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Residues in contact with LYS 119 (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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335A LEU* 3.9 27.5 - - + +
336A ALA 4.1 0.2 - - - +
338A SER 3.0 26.1 + - - +
339A GLY 4.6 9.8 - - - +
84C THR* 4.3 13.0 - - + +
85C LEU 3.1 18.4 - - - +
86C ILE* 3.3 33.1 - - + +
114C ILE* 4.1 4.0 - - - -
118C GLU* 1.3 75.6 - - - +
120C THR* 1.3 59.8 - - - +
121C ILE* 5.5 2.4 - - - +
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Residues in contact with THR 120 (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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333A SER* 4.1 0.9 + - - -
335A LEU* 2.1 33.4 + - - -
336A ALA* 3.6 1.2 - - - -
337A PRO* 3.6 18.8 - - - +
83C LEU 3.8 0.4 - - - +
84C THR* 3.3 1.4 - - - +
85C LEU* 3.0 32.7 + - + +
111C LEU 4.0 5.2 + - - -
112C THR* 3.9 29.6 - - + +
114C ILE* 3.6 22.0 - - + -
119C LYS* 1.3 76.0 - - - +
121C ILE* 1.3 75.9 + - - +
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Residues in contact with ILE 121 (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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333A SER* 3.6 3.1 - - - -
334A VAL* 2.9 38.5 + - + -
335A LEU* 3.0 36.6 + - + +
82C GLU* 3.5 32.1 - - + +
83C LEU 3.6 4.9 - - - +
84C THR* 2.9 33.0 - - + +
119C LYS* 5.5 2.9 - - - +
120C THR* 1.3 87.0 + - - +
122C LEU* 1.3 64.2 + - - +
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Residues in contact with LEU 122 (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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331A MET* 3.5 36.1 - - + -
332A THR 3.9 11.7 - - - +
333A SER* 4.4 5.2 - - - +
81C LEU* 3.5 2.6 - - - +
82C GLU* 3.4 2.3 - - - -
83C LEU* 3.0 35.6 + - + +
97C ILE* 5.1 8.3 - - + -
99C PHE* 5.2 6.1 - - + -
107C GLY 4.9 2.0 - - - +
108C GLY* 4.0 22.0 - - - -
111C LEU* 4.6 15.3 - - + +
112C THR* 3.8 22.4 - - + +
121C ILE* 1.3 75.8 - - - +
123C ARG* 1.3 65.3 + - - +
124C PHE* 4.6 16.6 - - + -
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Residues in contact with ARG 123 (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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328A ASP* 4.3 12.6 + - - +
329A ASP* 5.0 1.6 + - - +
330A LEU 4.7 0.2 - - - -
331A MET* 3.4 1.7 - - - +
332A THR* 3.0 61.6 + - - +
334A VAL* 4.0 14.6 - - + +
6C ALA* 5.8 1.4 - - - +
9C ILE* 3.3 43.2 - - - +
14C ARG* 5.0 5.0 - - - +
38C VAL* 4.3 12.3 - - - -
80C TYR* 3.9 30.3 - - + -
81C LEU 3.3 6.5 - - - +
82C GLU* 3.3 30.8 + - + +
121C ILE 4.3 0.2 + - - -
122C LEU* 1.3 77.9 - - - +
124C PHE* 1.3 63.7 + - - +
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Residues in contact with PHE 124 (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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329A ASP 5.1 0.2 - - - -
330A LEU 3.1 13.0 - - - +
331A MET* 4.2 10.3 - - + -
80C TYR* 3.2 7.5 - - - -
81C LEU* 3.0 67.2 + - + -
99C PHE* 4.6 21.1 - + + -
101C ALA* 3.7 19.1 - - + -
102C ALA* 3.8 27.4 - - + -
122C LEU* 4.6 13.2 - - + -
123C ARG* 1.3 76.5 - - - +
125C LYS* 1.3 70.6 + - - +
126C ALA* 4.0 18.4 - - + -
154C ILE* 4.0 21.3 - - + -
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Residues in contact with LYS 125 (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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329A ASP* 3.5 23.7 + - - +
330A LEU* 2.9 17.5 + - + +
4C ALA* 4.8 5.5 - - - +
78C ASP* 3.6 26.7 - - - +
80C TYR* 2.9 53.0 + - + +
101C ALA 4.2 3.6 - - - +
102C ALA* 5.0 1.9 - - - -
103C THR 5.5 1.0 + - - -
124C PHE* 1.3 80.2 - - - +
126C ALA* 1.3 63.7 + - - +
127C THR* 3.0 34.2 + - + +
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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