Contacts of the helix formed by residues 77 - 87 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLY* 3.6 21.4 - - - -
19A TYR* 3.6 2.9 - - - +
20A LEU* 4.0 13.5 - - - -
72A PRO 2.6 15.1 + - - -
73A ILE 3.1 6.7 + - - -
76A GLY* 1.3 73.1 - - - +
78A PHE* 1.3 66.5 + - - +
79A GLY 3.1 0.8 + - - -
81A TRP* 3.2 25.2 + - - +
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Residues in contact with PHE 78 (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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20A LEU* 4.3 6.3 - - + +
73A ILE* 2.9 48.3 + - + -
74A MET* 3.5 12.6 - - + +
77A GLY* 1.3 72.9 - - - -
79A GLY* 1.3 62.1 - - - +
81A TRP* 4.6 3.4 - - - -
82A LEU* 3.2 39.1 + - + +
184A PHE* 3.6 15.0 - - + -
253A MET* 4.1 18.6 - - + -
389A ILE* 4.1 11.2 - - + -
392A GLY* 3.7 21.1 - - - -
393A PHE* 3.6 33.9 - + + -
396A TRP* 4.2 4.0 - + - -
400A PHE* 3.8 30.7 - + - -
515A HEA 6.0 0.2 - - + -
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Residues in contact with GLY 79 (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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74A MET 3.3 7.7 + - - -
75A ILE* 3.0 21.1 + - - -
78A PHE* 1.3 77.9 - - - +
80A ASN* 1.3 56.4 + - - +
83A VAL* 3.0 42.3 + - - +
164A PHE* 3.5 13.4 - - - -
184A PHE* 4.2 5.8 - - - -
188A VAL* 5.0 3.6 - - - -
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Residues in contact with ASN 80 (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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12A HIS* 2.7 40.6 + - - +
15A ILE* 4.1 2.3 - - - +
16A GLY* 3.8 4.7 - - - -
19A TYR* 3.6 21.4 - - - -
75A ILE 3.6 0.8 + - - -
76A GLY* 2.8 28.8 + - - +
77A GLY 3.5 1.4 + - - -
79A GLY* 1.3 73.8 - - - +
81A TRP* 1.3 62.9 + - - +
84A PRO* 3.2 10.3 - - - +
92A MET* 3.7 15.2 - - - +
98A ASN* 2.8 37.2 + - - +
164A PHE* 4.0 12.6 - - - -
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Residues in contact with TRP 81 (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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12A HIS* 3.6 9.7 - - - -
13A LYS* 3.5 29.7 + - + -
16A GLY* 3.7 24.9 - - - -
17A THR* 2.9 27.8 + - - +
20A LEU* 4.4 10.1 - - + +
77A GLY 3.2 14.1 + - - +
78A PHE 4.3 1.3 - - - +
80A ASN* 1.3 80.7 - - - +
82A LEU* 1.3 60.4 + - - +
85A LEU* 3.3 34.3 - - + +
399A LEU* 4.3 2.9 - - + -
400A PHE* 3.4 71.5 - + + +
499A PRO* 4.9 0.2 - - + -
500A PRO* 3.6 34.5 - - + -
10L ASN* 4.1 13.5 - - - -
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Residues in contact with LEU 82 (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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78A PHE* 3.2 29.9 + - + +
81A TRP* 1.3 81.9 - - + +
83A VAL* 1.3 65.8 + - - +
84A PRO 3.4 0.9 - - - -
85A LEU* 3.2 3.6 + - + -
86A MET* 2.9 32.9 + - + +
184A PHE* 4.1 22.7 - - + -
396A TRP* 3.9 54.7 - - + +
399A LEU* 3.9 21.3 - - + -
400A PHE* 4.1 9.6 - - + -
493A GLU* 4.2 9.9 - - + -
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Residues in contact with VAL 83 (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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79A GLY* 3.0 28.8 + - - +
82A LEU* 1.3 77.2 - - - +
84A PRO* 1.3 70.3 - - + +
86A MET* 3.2 9.0 + - - +
87A ILE* 3.3 15.6 + - + +
92A MET* 5.0 0.2 - - - -
164A PHE* 4.0 10.5 - - + -
167A THR* 4.5 10.8 - - + -
168A ILE* 3.8 29.2 - - + -
184A PHE* 4.1 6.5 - - + -
185A VAL* 4.5 14.5 - - + +
188A VAL* 4.0 33.7 - - + -
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Residues in contact with PRO 84 (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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12A HIS* 3.7 29.6 - - + +
79A GLY 4.0 0.7 - - - +
80A ASN 3.2 17.0 - - - +
81A TRP 4.1 0.2 - - - +
82A LEU 3.7 0.7 - - - -
83A VAL* 1.3 94.7 - - + +
85A LEU* 1.3 63.0 + - - +
87A ILE* 3.2 3.8 + - + -
88A GLY 3.0 5.5 + - - -
89A ALA* 3.0 52.7 + - + +
91A ASP 4.3 8.3 - - - +
92A MET* 3.8 22.9 - - - -
167A THR* 5.2 2.2 - - + -
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Residues in contact with LEU 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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12A HIS* 4.1 12.1 - - + +
13A LYS* 4.2 4.5 - - - -
81A TRP* 3.3 41.1 - - + +
82A LEU* 3.2 6.8 + - - +
84A PRO* 1.3 78.0 - - - +
86A MET* 1.3 59.1 + - - +
87A ILE 3.5 0.2 + - - -
88A GLY 3.7 0.9 + - - -
89A ALA 5.3 0.2 - - - +
399A LEU* 4.5 10.3 - - + -
492A LEU* 3.0 26.9 - - - +
493A GLU* 3.9 32.8 + - + +
496A ASN* 5.5 2.2 - - + +
500A PRO* 4.3 12.8 - - + -
504A THR* 3.6 28.5 - - + +
505A PHE* 3.9 19.0 - - + -
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Residues in contact with MET 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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82A LEU* 2.9 29.3 + - + +
83A VAL 3.2 0.6 + - - +
85A LEU* 1.3 76.2 - - - +
87A ILE* 1.3 62.3 + - - +
88A GLY 3.6 0.4 - - - -
176A MET* 4.9 2.1 - - - +
182A PRO* 4.0 21.2 - - + +
184A PHE* 4.0 20.4 - - + -
185A VAL* 3.8 28.3 - - + -
256A HIS* 3.2 39.3 - - + +
396A TRP* 4.2 11.2 - - + -
492A LEU* 3.8 18.0 - - - +
493A GLU* 3.7 34.3 - - + +
71F TRP* 5.1 5.0 + - - -
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Residues in contact with ILE 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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83A VAL* 3.3 17.5 + - + +
84A PRO* 3.2 4.9 + - + +
86A MET* 1.3 80.8 - - - +
88A GLY* 1.3 61.8 + - - +
89A ALA* 4.2 10.8 - - + -
167A THR* 4.1 22.0 - - + +
168A ILE* 4.3 10.3 - - - -
171A MET 3.8 19.6 - - - +
172A LYS* 4.1 13.5 - - + -
173A PRO* 3.2 25.1 - - - +
176A MET* 3.6 28.9 - - + -
181A THR* 4.2 6.3 - - + -
182A PRO* 4.7 0.2 - - + -
185A VAL* 4.2 24.9 - - + -
492A LEU* 4.5 2.2 - - - -
71F 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