Contacts of the strand formed by residues 195 - 205 (chain C) in PDB entry 1PR1
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 LYS 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C LYS* 3.1 10.1 + - + +
84C LYS* 3.5 24.5 - - + +
85C ILE* 3.0 22.7 + - - +
130C ASP* 3.4 41.9 + - + +
132C ASP* 5.8 1.2 + - - -
133C MET* 3.8 8.3 - - - -
189C ALA* 4.3 2.0 - - - +
194C ALA* 1.3 82.3 - - - +
196C ALA* 1.3 64.0 + - - +
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Residues in contact with ALA 196 (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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85C ILE* 3.1 15.9 - - + +
129C ALA* 3.3 8.0 - - - +
130C ASP* 3.2 26.1 + - - +
133C MET* 3.9 5.4 - - - -
185C ILE* 3.8 28.3 - - + -
186C TYR* 3.9 9.6 - - + -
189C ALA* 4.0 16.7 - - + +
195C LYS* 1.3 79.0 - - - +
197C LEU* 1.3 62.8 + - - +
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Residues in contact with LEU 197 (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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85C ILE 2.9 6.3 + - - +
86C ILE* 3.1 12.5 - - + +
87C ARG* 2.7 30.7 + - - +
105C ILE* 3.8 15.3 - - + -
106C GLY 4.0 4.3 - - - +
129C ALA* 3.7 7.9 - - + -
133C MET* 3.6 39.5 - - + +
134C VAL* 3.5 32.3 - - + +
137C ALA* 3.7 19.3 - - + -
185C ILE* 6.0 0.7 - - - +
186C TYR* 3.7 4.9 - - - -
196C ALA* 1.3 76.1 - - - +
198C THR* 1.3 64.2 + - - +
199C ILE* 3.9 17.7 - - + -
231C SER* 5.5 2.9 - - - +
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Residues in contact with THR 198 (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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87C ARG* 3.5 39.7 - - + +
104C VAL 4.0 0.3 - - - +
105C ILE* 3.8 1.9 - - - -
106C GLY 3.0 25.5 + - - -
153C LEU* 3.7 23.4 - - + +
182C ALA* 3.5 21.8 - - + +
185C ILE* 4.8 2.6 - - - +
186C TYR* 2.9 24.9 + - - -
197C LEU* 1.3 78.8 - - - +
199C ILE* 1.3 65.9 + - - +
200C CYS* 3.7 9.6 - - - -
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Residues in contact with ILE 199 (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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86C ILE* 3.8 22.7 - - + -
87C ARG 2.7 14.4 + - - +
88C VAL* 3.3 2.2 - - + -
89C GLY 3.0 23.6 + - - +
103C VAL* 3.9 22.0 - - + -
104C VAL 3.4 9.6 - - - +
105C ILE* 4.7 7.9 - - + -
137C ALA* 4.5 3.6 - - + -
197C LEU* 3.9 21.5 - - + -
198C THR* 1.3 77.7 - - - +
200C CYS* 1.3 64.6 + - - +
224C MET* 3.8 20.6 - - + +
227C ILE* 4.2 12.8 - - + -
228C ALA* 3.9 27.1 - - + +
231C SER* 5.3 0.7 - - - +
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Residues in contact with CYS 200 (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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87C ARG* 3.7 27.1 - - - -
89C GLY 3.0 9.0 - - - +
90C SER 4.0 4.5 - - - -
91C CYS* 3.6 22.0 - - + -
102C ASP 3.7 0.5 - - - +
103C VAL* 3.4 5.6 - - - +
104C VAL* 2.8 40.2 + - + +
153C LEU* 4.1 13.5 - - + -
179C GLU* 4.1 6.3 - - - -
198C THR* 3.7 16.4 - - - -
199C ILE* 1.3 80.9 - - - +
201C THR* 1.3 63.0 + - - +
202C VAL 4.0 0.4 + - - -
224C MET* 4.2 1.8 - - - -
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Residues in contact with THR 201 (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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89C GLY 2.9 7.0 + - - -
90C SER* 3.2 5.9 - - - -
91C CYS* 3.1 15.5 + - - -
101C ARG* 4.0 25.1 - - - +
102C ASP 3.5 3.1 - - - -
103C VAL* 4.7 3.2 - - + +
200C CYS* 1.3 73.0 + - - +
202C VAL* 1.3 64.1 + - - +
203C SER* 2.8 10.7 + - - -
220C THR* 3.6 11.6 + - + +
221C PHE* 3.5 44.2 - - + -
224C MET* 3.2 30.2 - - - +
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Residues in contact with VAL 202 (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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91C CYS* 3.5 18.8 - - - +
93C ALA* 3.5 22.4 - - + +
98C VAL* 3.8 20.0 - - + -
99C LYS 3.7 17.3 - - - +
100C LEU* 3.7 8.8 - - + +
101C ARG* 2.9 23.0 + - - -
102C ASP* 2.9 24.6 + - + +
104C VAL* 4.2 11.0 - - + -
176C LEU 5.1 1.1 - - - +
200C CYS 4.0 0.4 - - - -
201C THR* 1.3 70.4 - - - +
203C SER* 1.3 58.2 + - - +
204C ASP 3.5 22.2 - - - +
205C HIS* 5.5 0.2 - - + -
211C GLN* 4.7 1.7 + - - -
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Residues in contact with SER 203 (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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90C SER* 3.4 28.3 + - - -
91C CYS 2.8 7.0 + - - -
100C LEU* 3.6 4.7 - - - +
201C THR 2.8 4.9 + - - -
202C VAL* 1.3 72.1 - - - +
204C ASP* 1.3 73.2 + - - +
211C GLN* 3.1 48.6 + - - +
215C ALA* 5.1 3.8 - - - -
221C PHE* 3.9 6.3 - - - -
247C FMB 3.6 5.9 + - - -
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Residues in contact with ASP 204 (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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91C CYS 3.4 0.2 + - - -
92C GLY* 3.3 5.5 - - - -
93C ALA 2.9 22.2 + - - -
100C LEU* 3.3 14.5 - - - +
159C PHE* 5.3 4.8 - - - -
202C VAL* 3.5 7.3 - - - +
203C SER* 1.3 85.2 + - - +
205C HIS* 1.3 63.4 + - - +
206C ILE* 3.8 9.0 - - - +
209C HIS 4.6 0.2 - - - -
210C GLU* 3.3 31.4 - - + +
247C FMB 2.8 46.6 + - - +
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Residues in contact with HIS 205 (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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93C ALA* 3.5 23.5 - - + +
94C VAL 4.2 7.9 - - - -
95C LEU 3.0 26.8 + - - -
96C PRO* 4.5 6.5 + - + +
98C VAL 3.3 21.4 + - - -
99C LYS* 5.4 2.5 - - - -
100C LEU* 4.8 5.4 - - + -
202C VAL* 5.5 0.7 - - + -
204C ASP* 1.3 78.6 - - - +
206C ILE* 1.3 66.2 + - - +
207C ARG* 3.3 31.6 + - + -
208C THR* 3.0 45.8 + - - +
209C HIS* 3.3 11.2 + - - +
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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