Contacts of the strand formed by residues 84 - 92 (chain C) in PDB entry 1P27
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 GLY 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C GLY 3.2 11.7 - - - -
81C ASP* 3.0 36.2 + - - +
83C VAL* 1.3 81.8 - - - +
85C ARG* 1.3 60.4 + - - +
102C SER* 3.7 4.7 - - - -
103C LYS* 3.7 22.2 - - - -
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Residues in contact with ARG 85 (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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47A ARG* 4.0 28.1 + - - +
10C TYR* 3.8 17.6 - - + -
11C VAL* 3.4 3.6 - - - +
12C GLY* 2.9 33.0 + - - +
80C PRO* 3.9 30.1 - - + +
81C ASP 5.2 1.3 - - - +
84C GLY* 1.3 75.5 - - - +
86C GLN* 1.3 72.9 + - - +
87C GLU* 3.1 29.8 + - - -
100C THR* 3.6 19.4 + - - +
101C THR 3.2 7.6 - - - +
102C SER 4.1 1.1 - - - -
103C LYS* 3.8 2.2 - - - +
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Residues in contact with GLN 86 (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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9C TYR* 2.6 36.5 + - + +
10C TYR 3.2 6.7 - - - +
11C VAL* 3.8 13.0 - - + +
85C ARG* 1.3 79.8 - - - +
87C GLU* 1.3 65.0 + - - +
99C PHE 4.0 0.4 - - - +
100C THR* 3.4 4.2 - - - -
101C THR* 2.9 34.7 + - - +
102C SER 3.1 21.0 + - - +
103C LYS* 4.2 1.6 - - - -
104C ILE* 3.4 26.1 + - - +
122C PHE* 3.6 35.4 - - + -
126C VAL* 4.1 7.7 - - - +
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Residues in contact with GLU 87 (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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33A ARG* 3.8 2.4 + - - -
47A ARG* 2.8 37.5 + - - +
49A GLU* 5.5 3.1 - - - -
8C ARG* 2.8 38.7 + - - +
9C TYR* 3.3 12.5 - - - -
10C TYR* 2.9 36.4 + - + +
85C ARG* 3.1 34.6 + - - +
86C GLN* 1.3 79.2 - - - +
88C LEU* 1.3 59.8 + - - +
89C GLU 4.3 0.2 - - - -
99C PHE 3.3 5.8 - - - +
100C THR* 4.2 9.9 - - - +
122C PHE* 5.5 0.9 - - - -
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Residues in contact with LEU 88 (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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7C LEU* 4.3 11.4 - - + -
8C ARG 3.4 18.8 - - - +
9C TYR* 4.5 10.8 - - + -
69C ILE* 4.4 1.1 - - + -
87C GLU* 1.3 76.3 - - - +
89C GLU* 1.3 64.5 + - - +
90C ILE* 3.9 33.4 - - + -
97C ILE 4.0 0.3 - - - +
98C SER* 3.3 4.4 + - - -
99C PHE* 2.8 58.7 + - + +
122C PHE* 3.9 28.4 - - + -
125C LEU* 4.2 17.7 - - + -
126C VAL* 4.9 2.2 - - + -
129C LEU* 4.3 11.0 - - + -
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Residues in contact with GLU 89 (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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27A ARG* 2.8 44.4 + - - -
31A LYS* 4.2 9.1 + - - -
33A ARG* 4.7 1.2 + - - -
49A GLU* 5.2 0.4 - - - +
6C TYR* 3.7 12.8 - - + -
7C LEU* 3.3 4.2 - - - -
8C ARG* 2.9 60.8 + - + +
87C GLU 4.3 0.2 - - - -
88C LEU* 1.3 74.2 - - - +
90C ILE* 1.3 63.4 + - - +
96C HIS* 3.3 30.4 - - + +
97C ILE 3.4 3.8 - - - +
98C SER* 3.8 17.9 + - - +
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Residues in contact with ILE 90 (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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5C PHE* 4.8 0.4 - - + -
6C TYR 3.3 9.2 - - - +
7C LEU* 3.9 20.9 - - + -
64C ILE* 4.2 20.4 - - + -
69C ILE* 4.1 24.5 - - + -
88C LEU* 3.9 27.1 - - + -
89C GLU* 1.3 79.6 - - - +
91C VAL* 1.3 60.2 + - - +
92C ILE* 3.3 31.2 - - + -
95C GLU 3.9 0.2 - - - +
96C HIS* 2.3 29.8 - - - -
97C ILE* 3.0 33.4 + - + +
99C PHE* 5.4 1.1 - - + -
125C LEU* 4.5 2.5 - - + -
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Residues in contact with VAL 91 (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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4C ASP* 4.5 13.2 - - + +
5C PHE* 3.3 9.5 - - - -
6C TYR* 2.9 50.5 + - + +
90C ILE* 1.3 73.6 - - - +
92C ILE* 1.3 60.1 + - - +
93C GLY 3.5 20.0 - - - +
94C ASP* 5.4 1.3 - - - -
95C GLU 3.5 9.0 - - - +
96C HIS* 2.7 43.3 + - + +
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Residues in contact with ILE 92 (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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4C ASP 4.0 2.0 - - - -
5C PHE* 3.7 25.6 - - + -
61C LYS* 3.9 23.8 - - + +
64C ILE* 4.2 12.3 - - + -
65C ASP* 5.1 10.5 - - - +
70C THR* 3.4 26.5 - - + -
90C ILE* 3.3 20.4 - - + -
91C VAL* 1.3 70.6 - - - +
93C GLY* 1.3 65.8 + - - +
94C ASP 3.1 3.1 + - - -
95C GLU* 3.0 50.4 + - + +
97C ILE* 4.3 3.1 - - + -
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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