Contacts of the helix formed by residues 54 - 63 (chain U) 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 GLU 54 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8U ILE 5.5 6.7 - - - +
9U LYS* 6.0 4.3 - - + +
36U PHE* 5.0 2.3 - - - -
50U VAL 3.5 5.1 + - - +
51U SER* 3.7 20.7 - - - +
52U VAL 3.1 1.2 - - - -
53U CYS* 1.3 76.2 - - - +
55U TRP* 1.3 56.4 + - - +
57U ARG* 2.5 77.8 + - - +
58U ARG* 3.1 25.8 + - + +
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Residues in contact with TRP 55 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H LYS* 4.1 27.1 - - - -
8U ILE* 4.2 43.5 + - + -
11U TYR* 3.9 25.6 - + - -
15U PRO* 4.1 30.3 - - + -
32U ASN* 5.1 2.0 + - - -
52U VAL 4.0 2.9 + - - +
53U CYS 3.4 0.2 - - - -
54U GLU* 1.3 77.3 - - - +
56U TYR* 1.3 91.0 + + + +
58U ARG* 3.0 18.8 + - + +
59U VAL* 3.0 33.7 + - + +
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Residues in contact with TYR 56 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H LYS* 5.0 10.8 + - + -
19U ARG* 6.0 2.2 - - - -
32U ASN* 3.5 26.1 - - - +
35U ASP* 4.0 26.2 + - + -
36U PHE* 3.5 33.4 - - + -
39U CYS* 4.7 12.6 - - + -
52U VAL 4.9 5.4 - - - -
53U CYS* 3.4 16.6 + - - +
54U GLU 3.0 0.8 + - - -
55U TRP* 1.3 97.1 - + + +
57U ARG* 1.3 58.5 + - - +
59U VAL* 3.8 3.5 - - - +
60U TYR* 2.8 35.3 + - - +
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Residues in contact with ARG 57 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U PHE* 3.7 31.1 - - + -
53U CYS 3.6 1.4 + - - -
54U GLU* 2.5 60.3 + - - +
56U TYR* 1.3 71.5 - - - +
58U ARG* 1.3 78.0 + - - +
60U TYR* 3.5 33.2 - - + +
61U LYS* 2.8 46.4 + - + +
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Residues in contact with ARG 58 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O ASP 2.9 29.6 + - - +
113O TYR* 4.0 22.0 + - - +
8U ILE 5.9 2.9 - - - +
9U LYS* 4.8 15.0 + - - +
11U TYR* 3.0 55.2 + - + +
54U GLU* 3.1 27.1 + - + +
55U TRP* 3.0 11.5 + - + +
57U ARG* 1.3 100.2 - - - +
59U VAL* 1.3 52.1 + - - +
61U LYS* 3.1 7.2 + - - +
62U SER* 2.8 32.1 + - - -
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Residues in contact with VAL 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U TYR* 3.3 16.4 - - + +
14U ALA* 4.1 11.2 - - + -
15U PRO* 5.0 0.7 - - + -
28U ASN* 4.6 0.9 - - - +
32U ASN* 3.3 33.9 - - - +
55U TRP* 3.0 49.1 + - + +
56U TYR 3.8 3.6 - - - +
58U ARG* 1.3 73.4 - - - +
60U TYR* 1.3 68.0 + - - +
62U SER* 3.0 12.6 + - - -
63U LEU* 3.0 28.6 + - + +
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Residues in contact with TYR 60 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U CYS* 4.7 0.7 - - - +
32U ASN* 3.7 10.3 - - + -
33U TYR* 3.6 48.2 - + - +
36U PHE* 3.7 16.9 - + + -
37U HIS* 3.7 16.0 + + - -
56U TYR 2.8 26.5 + - - +
57U ARG* 3.5 33.7 - - + +
59U VAL* 1.3 76.1 - - - +
61U LYS* 1.3 69.9 + - + +
63U LEU* 4.6 2.2 - - - +
64U CYS* 2.7 51.7 + - - +
69U VAL* 3.7 32.2 - - + +
73U ASP* 4.9 2.4 + - - -
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Residues in contact with LYS 61 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98O LYS* 3.9 6.4 + - - -
111O THR* 2.7 36.3 + - - +
112O ASP 6.0 0.2 - - - +
115O ASP* 3.7 32.0 + - - +
57U ARG* 2.8 40.3 + - + +
58U ARG* 3.3 8.7 - - - +
60U TYR* 1.3 98.1 - - + +
62U SER* 1.3 57.6 + - - +
64U CYS* 3.9 2.5 - - - +
66U ILE* 4.6 11.7 - - + +
69U VAL* 4.7 16.1 - - + +
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Residues in contact with SER 62 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96O THR* 3.8 14.4 - - - +
98O LYS* 3.3 22.5 - - - -
111O THR* 3.4 10.8 + - - -
112O ASP* 2.7 30.4 + - - -
11U TYR* 2.5 33.3 + - - -
13U THR* 4.2 5.6 - - - -
14U ALA* 4.4 6.7 - - - -
58U ARG 2.8 8.2 + - - -
59U VAL 3.4 4.0 - - - -
61U LYS* 1.3 77.7 - - - +
63U LEU* 1.3 59.3 + - - +
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Residues in contact with LEU 63 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96O THR* 4.5 2.5 - - + +
98O LYS* 3.5 10.1 - - - +
151O ARG* 4.0 28.7 - - - +
153O LEU* 3.7 24.8 - - + +
179O LEU* 3.4 19.4 - - + +
14U ALA* 4.0 11.2 - - + -
25U GLN* 5.5 4.5 - - + +
28U ASN* 3.6 42.8 - - + +
29U CYS* 4.4 11.0 - - + +
59U VAL* 3.0 30.7 + - + +
60U TYR 4.4 0.7 - - - +
62U SER* 1.3 78.6 - - - +
64U CYS* 1.3 64.7 + - - +
65U PRO 3.5 0.9 - - - -
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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