Contacts of the helix formed by residues 77 - 87 (chain N) in PDB entry 1OCR
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 77 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16N GLY* 3.6 20.8 - - - -
19N TYR* 3.8 3.4 - - - -
20N LEU* 4.0 13.9 - - - -
72N PRO 2.6 15.3 + - - -
73N ILE 3.1 8.6 + - - -
76N GLY* 1.3 72.8 - - - +
78N PHE* 1.3 64.6 + - - -
79N GLY 3.1 0.6 + - - -
81N TRP* 3.1 25.2 + - - +
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Residues in contact with PHE 78 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20N LEU* 4.2 7.6 - - + +
73N ILE* 2.9 49.6 + - + -
74N MET* 3.5 11.4 - - + +
77N GLY* 1.3 71.9 - - - -
79N GLY* 1.3 62.5 - - - +
81N TRP* 4.0 4.0 - - - -
82N LEU* 3.1 39.4 + - + +
184N PHE* 3.6 16.0 - - + -
253N MET* 4.0 17.5 - - + -
389N ILE* 4.0 11.2 - - + -
392N GLY* 3.7 21.1 - - - -
393N PHE* 3.6 33.9 - + + -
396N TRP* 4.2 5.4 - + - -
400N PHE* 3.8 28.7 - + - -
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Residues in contact with GLY 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N MET 3.3 7.2 + - - -
75N ILE* 3.0 22.0 + - - -
78N PHE* 1.3 76.5 - - - +
80N ASN* 1.3 56.8 + - - +
83N VAL* 3.0 42.8 + - - +
164N PHE* 3.5 14.1 - - - -
184N PHE* 4.3 6.5 - - - -
188N VAL* 5.0 3.1 - - - -
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Residues in contact with ASN 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N HIS* 2.8 42.0 + - - +
15N ILE* 4.2 2.8 - - - +
16N GLY* 3.8 4.5 - - - -
19N TYR* 3.6 21.6 - - - -
75N ILE 3.6 0.8 + - - -
76N GLY* 2.8 30.6 + - - +
77N GLY 3.4 1.6 + - - -
79N GLY* 1.3 72.0 - - - +
81N TRP* 1.3 63.5 + - - +
84N PRO* 3.2 10.7 - - - +
92N MET* 3.7 15.3 - - - +
98N ASN* 2.8 36.4 + - - +
164N PHE* 4.0 12.3 - - - -
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Residues in contact with TRP 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N HIS* 3.6 9.4 - - - -
13N LYS* 3.6 28.9 + - + -
16N GLY* 3.7 25.4 - - - -
17N THR* 2.9 28.7 + - - +
20N LEU* 4.4 9.8 - - + +
77N GLY 3.1 13.6 + - - +
78N PHE 4.2 1.3 - - - +
80N ASN* 1.3 82.1 - - - +
82N LEU* 1.3 60.1 + - - +
85N LEU* 3.3 34.9 - - + +
399N LEU* 4.3 2.2 - - + -
400N PHE* 3.4 71.2 - + + +
500N PRO* 3.6 35.4 - - + -
10Y ASN* 4.2 11.2 - - - -
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Residues in contact with LEU 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N PHE* 3.1 32.9 + - + +
81N TRP* 1.3 82.4 - - + +
83N VAL* 1.3 67.2 + - - +
84N PRO 3.4 1.1 - - - -
85N LEU* 3.1 4.7 + - + -
86N MET* 2.8 34.8 + - + +
184N PHE* 4.0 20.2 - - + -
396N TRP* 3.9 51.4 - - + +
399N LEU* 4.0 20.4 - - + -
400N PHE* 4.1 9.4 - - + -
493N GLU* 4.2 9.6 - - + -
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Residues in contact with VAL 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N GLY* 3.0 31.5 + - - +
82N LEU* 1.3 72.8 - - - +
84N PRO* 1.3 68.9 - - + +
86N MET* 3.2 9.9 + - - +
87N ILE* 3.3 17.1 + - + +
92N MET* 5.0 0.4 - - - -
164N PHE* 4.0 16.6 - - + -
167N THR* 4.5 11.2 - - + -
168N ILE* 3.8 29.6 - - + -
184N PHE* 4.3 7.0 - - + -
185N VAL* 4.4 14.8 - - + +
188N VAL* 4.0 26.7 - - + -
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Residues in contact with PRO 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N HIS* 3.7 30.3 - - + +
79N GLY 4.1 0.7 - - - +
80N ASN 3.2 17.0 - - - +
81N TRP 4.2 0.2 - - - +
82N LEU 3.7 0.4 - - - -
83N VAL* 1.3 96.2 - - + +
85N LEU* 1.3 61.6 + - - +
87N ILE* 3.3 3.3 + - + -
88N GLY 3.0 5.7 + - - -
89N ALA* 2.9 53.9 + - + +
91N ASP 4.4 7.6 - - - +
92N MET* 3.8 22.4 - - - -
167N THR* 5.1 2.5 - - + -
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Residues in contact with LEU 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N HIS* 4.0 11.2 - - + +
13N LYS* 4.2 4.7 - - - -
81N TRP* 3.3 39.7 - - + +
82N LEU* 3.1 8.1 + - - +
84N PRO* 1.3 76.6 - - - +
86N MET* 1.3 58.2 + - - +
88N GLY 3.7 1.0 + - - -
399N LEU* 4.4 6.7 - - + -
492N LEU* 2.9 27.0 - - - +
493N GLU* 3.9 36.1 + - + +
496N ASN* 5.5 2.2 - - + +
500N PRO* 4.3 13.0 - - + -
504N THR* 3.6 29.2 - - + +
505N PHE* 3.9 18.2 - - + -
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Residues in contact with MET 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N LEU* 2.8 29.1 + - + +
83N VAL 3.2 0.6 + - - +
85N LEU* 1.3 77.0 - - - +
87N ILE* 1.3 63.3 + - - +
88N GLY 3.5 0.4 - - - -
176N MET* 4.8 2.3 - - - +
182N PRO* 4.0 21.0 - - + +
184N PHE* 4.0 19.7 - - + -
185N VAL* 3.8 29.2 - - + -
256N HIS* 3.3 39.5 - - + +
396N TRP* 4.2 11.2 - - + -
492N LEU* 3.7 17.6 - - + +
493N GLU* 3.7 33.9 - - + +
71S TRP* 5.0 5.0 + - - -
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Residues in contact with ILE 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N VAL* 3.3 19.2 + - + +
84N PRO* 3.3 7.6 + - + +
86N MET* 1.3 81.3 - - - +
88N GLY* 1.3 62.0 + - - +
89N ALA* 4.2 8.3 - - + -
167N THR* 4.1 24.5 - - + +
168N ILE* 4.3 9.9 - - + +
171N MET 3.8 20.0 - - - +
172N LYS* 4.1 10.5 - - + -
173N PRO* 3.2 24.3 - - - +
176N MET* 3.6 29.4 - - + -
181N THR* 4.2 12.3 - - + -
182N PRO* 4.7 0.2 - - + -
185N VAL* 4.2 17.7 - - + -
492N LEU* 4.5 2.0 - - - -
71S TRP* 5.8 1.1 - - - -
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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