Contacts of the strand formed by residues 84 - 92 (chain A) 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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASP 3.0 3.6 + - - -
15A VAL* 3.4 27.4 - - + -
16A VAL 3.1 23.7 + - - -
55A ARG* 6.1 1.0 - - - +
82A VAL* 3.3 7.8 - - - +
83A LYS* 1.3 87.4 - - + +
85A ILE* 1.3 63.5 + - - +
130A ASP* 5.5 0.2 - - - -
132A ASP* 6.2 1.2 - - - +
133A MET* 3.8 42.2 - - + +
136A ASN* 4.5 3.4 - - - +
195A LYS* 3.3 24.2 - - + +
232A VAL* 4.9 13.9 + - + +
235A GLY* 4.2 27.5 + - - -
236A ASP* 5.3 2.8 + - - -
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.6 12.8 - - + +
18A MET* 4.1 18.8 - - + -
73A THR* 3.4 45.1 - - + +
76A LEU* 4.6 9.2 - - + -
77A ILE* 4.2 15.3 - - + -
82A VAL* 4.0 12.8 - - + -
83A LYS 5.7 0.2 - - - -
84A LYS* 1.3 79.8 - - - +
86A ILE* 1.3 68.5 + - - +
87A ARG 4.5 1.8 - - - +
133A MET* 3.7 2.3 - - - +
185A ILE* 4.2 18.4 - - + -
194A ALA* 6.2 0.2 - - + -
195A LYS 2.9 12.5 + - - +
196A ALA* 3.2 6.4 - - + -
197A LEU 2.9 27.2 + - - +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 4.6 7.2 - - + -
16A VAL 3.1 8.1 + - - -
17A LEU* 3.3 24.7 - - + +
18A MET 2.8 24.9 + - - -
85A ILE* 1.3 73.9 - - - +
87A ARG* 1.3 67.9 + - - +
88A VAL* 3.7 2.9 + - + -
133A MET* 3.4 27.1 - - + -
197A LEU* 3.1 11.4 - - + +
199A ILE* 4.2 15.3 - - + -
228A ALA* 3.9 23.1 - - + +
231A SER* 3.9 8.3 - - - +
232A VAL* 3.7 31.4 - - + -
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 3.3 9.4 - - + +
20A GLY 4.2 3.4 - - - +
62A HIS* 3.0 34.1 + - + +
85A ILE* 4.0 2.2 - - - +
86A ILE* 1.3 74.4 - - - +
88A VAL* 1.3 62.8 + - - +
89A GLY* 4.0 12.6 - - - +
90A SER 3.7 11.5 + - - -
179A GLU* 3.4 20.2 + - - +
181A GLU* 3.2 24.4 + - - +
185A ILE* 3.7 26.2 - - + -
197A LEU 2.8 6.5 + - - +
198A THR* 3.2 22.2 - - + -
199A ILE 2.8 27.1 + - - +
200A CYS* 4.0 6.8 - - - -
245A FMB 2.7 24.5 + - - -
248A PO4 3.3 19.6 + - - -
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.9 5.2 - - + -
18A MET 3.1 22.7 + - - +
19A PRO* 3.4 27.4 - - + +
20A GLY 4.2 1.7 + - - -
28A ILE* 4.8 2.5 - - + -
86A ILE* 4.3 7.2 - - + +
87A ARG* 1.3 79.5 - - - +
89A GLY* 1.3 57.7 + - - +
199A ILE* 3.4 6.7 - - + +
221A PHE* 5.1 3.0 - - + -
224A MET* 3.7 32.8 - - + +
225A ILE* 3.8 21.8 - - + -
228A ALA* 3.8 26.5 - - + -
248A PO4 4.7 1.0 + - - -
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 6.3 0.2 - - - -
87A ARG* 4.0 9.5 - - - +
88A VAL* 1.3 73.6 - - - +
90A SER* 1.3 61.2 + - - -
199A ILE 3.0 9.5 + - - -
200A CYS* 3.1 7.3 - - - -
201A THR* 2.9 23.0 + - - -
221A PHE* 5.9 1.1 - - - -
224A MET* 3.4 14.9 - - - +
248A PO4 3.2 17.7 - - - -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 5.8 4.7 - - - -
87A ARG* 3.7 9.4 + - - -
89A GLY* 1.3 74.8 - - - -
91A CYS* 1.3 65.5 + - - +
179A GLU* 3.8 2.4 - - - +
200A CYS* 4.1 1.3 - - - -
201A THR* 3.3 14.1 - - - -
203A SER* 3.6 18.6 + - - -
217A ARG* 5.1 1.6 - - - -
245A FMB 2.6 40.6 + - - -
248A PO4 3.0 21.6 + - - -
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Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER* 1.3 78.2 - - - +
92A GLY* 1.3 60.8 + - - +
104A VAL* 4.8 6.5 - - - -
153A LEU* 5.0 1.1 - - + -
177A GLY* 3.8 20.4 - - - -
178A VAL 3.2 23.3 - - - +
179A GLU* 4.2 4.7 - - + -
200A CYS* 3.7 23.3 - - + -
201A THR 3.1 11.7 + - - -
202A VAL* 3.5 22.2 - - - -
203A SER* 2.9 27.5 + - - -
204A ASP 3.7 0.2 + - - -
245A FMB 3.4 9.6 - - - -
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Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A CYS* 1.3 76.7 - - - +
93A ALA* 1.3 62.1 + - - -
177A GLY* 3.2 3.7 - - - -
178A VAL* 2.6 45.6 + - - +
204A ASP* 3.0 20.6 - - - -
205A HIS* 5.3 0.9 - - - -
245A FMB 3.3 12.1 + - - -
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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