Contacts of the helix formed by residues 26 - 44 (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 THR 26 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O GLY 3.8 18.2 - - - +
178O ARG* 3.5 7.1 - - - +
179O LEU* 3.1 28.7 + - - +
110P PRO* 4.0 26.5 - - + -
24U ASN* 2.6 24.9 + - - -
25U GLN* 1.3 76.5 - - - +
27U ARG* 1.3 67.0 + - - +
29U CYS* 3.5 4.3 + - - +
30U TRP* 3.2 19.2 + - - +
68U TRP* 4.2 13.3 - - + -
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Residues in contact with ARG 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107P ALA* 5.3 1.2 - - - +
108P PRO* 2.9 32.1 + - - +
109P THR* 4.9 2.2 - - - +
110P PRO* 4.9 8.6 - - - +
114P GLY* 3.9 20.4 + - - -
20U PHE* 3.5 24.7 - - + -
24U ASN* 4.9 5.8 + - - +
25U GLN 3.0 1.4 + - - -
26U THR* 1.3 80.2 - - - +
28U ASN* 1.3 55.7 + - - +
30U TRP* 3.1 26.7 + - - +
31U GLN* 2.6 45.4 + - + +
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Residues in contact with ASN 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151O ARG* 6.2 0.8 - - - +
14U ALA* 6.0 0.4 - - - +
15U PRO 5.2 4.2 + - - -
17U ASP* 3.9 16.7 - - - +
20U PHE* 3.4 35.4 + - + +
25U GLN* 2.8 38.2 + - + +
27U ARG* 1.3 76.8 - - - +
29U CYS* 1.3 62.5 + - - +
32U ASN* 2.7 53.5 + - - -
59U VAL* 4.6 0.9 - - - +
63U LEU* 3.6 22.6 - - + +
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Residues in contact with CYS 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179O LEU* 3.9 22.2 - - + -
25U GLN 3.3 2.2 + - - -
26U THR 3.8 6.3 - - - +
27U ARG 3.3 0.4 - - - -
28U ASN* 1.3 80.4 - - - +
30U TRP* 1.3 67.8 + - - +
32U ASN* 3.1 3.1 + - - +
33U TYR 2.9 19.1 + - - -
60U TYR* 5.1 0.2 - - - +
63U LEU* 4.4 9.2 - - + +
64U CYS* 2.0 57.1 - - - +
68U TRP* 4.0 9.9 - - + -
72U TRP* 3.6 22.0 - - - -
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Residues in contact with TRP 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110P PRO* 3.3 56.8 - - + -
113P GLY 3.9 17.9 + - - -
114P GLY* 4.5 9.9 - - - -
26U THR 3.2 11.3 + - - +
27U ARG* 3.1 29.2 + - - +
29U CYS* 1.3 84.0 - - - +
31U GLN* 1.3 72.0 + - + +
33U TYR* 3.0 5.0 + + - +
34U LEU* 2.9 48.3 + - + +
72U TRP* 3.6 30.1 - + + -
81U PHE* 3.7 35.9 - + - -
82U PRO* 4.4 1.3 - - + -
83U GLY* 3.9 13.9 - - - -
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Residues in contact with GLN 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U ARG* 4.7 9.4 - - - +
20U PHE* 3.9 23.8 - - + -
27U ARG* 2.6 28.4 + - + +
28U ASN 4.3 0.7 - - - +
30U TRP* 1.3 81.4 - - + +
32U ASN* 1.3 59.7 + - - +
34U LEU* 3.0 11.0 + - - +
35U ASP* 2.8 62.7 + - - +
38U ARG* 3.5 18.2 - - - +
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Residues in contact with ASN 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U ASP* 4.8 1.6 + - - -
19U ARG* 4.4 15.7 + - - +
20U PHE* 4.9 0.6 - - - -
28U ASN* 2.7 41.9 + - - +
29U CYS 3.1 1.4 + - - -
31U GLN* 1.3 76.0 - - - +
33U TYR* 1.3 62.6 + - - +
35U ASP* 4.3 5.8 - - - +
36U PHE* 3.1 24.6 + - - +
55U TRP* 5.1 2.1 + - - -
56U TYR* 3.5 30.4 - - + +
59U VAL* 3.3 28.3 - - + +
60U TYR* 3.7 20.0 - - + +
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Residues in contact with TYR 33 (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 2.9 11.6 + - - +
30U TRP* 3.3 9.9 - + - +
32U ASN* 1.3 77.8 - - - +
34U LEU* 1.3 66.4 + - + +
36U PHE* 3.7 0.5 + - - +
37U HIS* 2.9 49.8 + + - -
60U TYR* 3.6 33.1 - + + +
64U CYS* 4.6 0.2 - - - -
69U VAL* 4.3 13.2 - - + -
72U TRP* 3.0 48.7 + + + +
73U ASP* 2.8 25.9 + - - -
76U ARG* 3.1 16.2 + - - -
81U PHE* 3.5 34.8 - + - -
85U ILE* 4.8 0.9 - - + -
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Residues in contact with LEU 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P GLY 5.8 0.7 - - - +
30U TRP* 2.9 45.9 + - + +
31U GLN* 3.3 12.6 - - - +
33U TYR* 1.3 76.3 - - + +
35U ASP* 1.3 68.1 + - - +
36U PHE 3.1 0.7 + - - -
37U HIS* 3.1 5.7 + - - +
38U ARG* 3.0 59.3 + - - +
81U PHE* 3.6 34.3 - - + -
83U GLY* 4.4 6.1 - - - -
84U LYS 4.4 2.2 - - - +
85U ILE* 3.7 14.6 - - + -
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Residues in contact with ASP 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U ARG* 5.1 4.5 + - - -
31U GLN* 2.8 47.8 + - - +
32U ASN* 4.0 5.6 - - - +
34U LEU* 1.3 73.8 - - - +
36U PHE* 1.3 62.9 + - - +
38U ARG* 3.1 18.4 + - - +
39U CYS* 2.8 23.9 + - - +
56U TYR* 4.0 33.8 + - + -
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Residues in contact with PHE 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32U ASN 3.1 13.6 + - - +
33U TYR 3.9 2.9 - - - +
34U LEU 3.1 0.2 + - - -
35U ASP* 1.3 75.0 - - - +
37U HIS* 1.3 102.4 + + - +
39U CYS* 2.9 3.3 + - - +
40U GLU* 2.7 57.3 + - + +
50U VAL* 5.6 1.3 - - + -
53U CYS* 3.1 37.7 - - + -
54U GLU* 5.0 1.6 - - - -
56U TYR* 3.5 21.9 - - + +
57U ARG* 3.7 35.2 - - + -
60U TYR* 3.7 14.6 - + + -
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Residues in contact with HIS 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33U TYR* 2.9 48.1 + + - +
34U LEU 3.1 5.4 + - - +
36U PHE* 1.3 107.6 - + - +
38U ARG* 1.3 58.0 + - - +
40U GLU* 3.8 16.9 + - - +
41U LYS* 3.1 26.3 + - - +
60U TYR* 3.7 10.4 + - - -
73U ASP* 4.2 1.0 + - - -
76U ARG* 2.9 43.9 + - - +
85U ILE* 3.7 29.0 - - + +
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Residues in contact with ARG 38 (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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31U GLN* 3.5 25.9 - - - +
34U LEU* 3.0 37.2 + - - +
35U ASP* 3.5 18.7 + - - +
37U HIS* 1.3 76.4 - - - +
39U CYS* 1.3 61.0 + - - +
41U LYS* 3.4 6.8 + - - +
42U ALA* 3.0 28.6 + - - +
84U LYS* 2.6 40.4 + - - +
85U ILE* 3.8 27.6 - - + +
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Residues in contact with CYS 39 (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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43H MET* 5.1 3.4 - - - -
35U ASP 2.8 17.0 + - - +
36U PHE* 3.5 4.3 - - - +
38U ARG* 1.3 73.0 - - - +
40U GLU* 1.3 64.2 + - - +
42U ALA* 3.1 5.8 + - - +
43U MET* 2.9 31.2 + - - +
52U VAL* 3.6 16.2 - - - -
53U CYS* 2.3 54.0 - - + -
56U TYR* 4.7 11.9 - - + -
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Residues in contact with GLU 40 (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* 2.7 45.8 + - + +
37U HIS* 3.8 22.4 + - - +
39U CYS* 1.3 76.4 - - - +
41U LYS* 1.3 57.0 + - - +
43U MET* 3.6 0.9 + - - -
44U THR* 3.0 41.9 + - - +
50U VAL* 4.0 13.0 - - + +
53U CYS* 3.0 13.2 - - + -
76U ARG* 4.7 3.5 + - - -
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Residues in contact with LYS 41 (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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37U HIS 3.1 17.7 + - - +
38U ARG* 3.7 6.2 + - - +
39U CYS 3.2 0.2 - - - -
40U GLU* 1.3 81.7 - - - +
42U ALA* 1.3 58.7 + - - +
44U THR* 3.2 5.0 + - - -
45U ALA* 2.7 46.8 + - + +
85U ILE* 3.8 37.4 + - + +
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Residues in contact with ALA 42 (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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38U ARG 3.0 17.4 + - - +
39U CYS* 3.6 5.4 - - - +
41U LYS* 1.3 79.8 - - - +
43U MET* 1.3 73.9 + - + +
45U ALA* 3.0 5.9 + - - -
46U LYS* 2.9 43.6 + - + +
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Residues in contact with MET 43 (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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39H CYS* 5.1 3.1 - - - -
43H MET* 3.3 44.2 - - + +
49H ASP* 4.4 0.4 - - - +
52H VAL* 3.9 28.0 - - + -
39U CYS* 2.9 24.5 + - - +
42U ALA* 1.3 85.3 - - + +
44U THR* 1.3 56.9 + - - +
46U LYS 4.2 0.4 - - - -
48U GLY* 2.7 37.5 + - - +
49U ASP* 3.2 37.5 - - - +
50U VAL* 4.0 8.7 - - + -
52U VAL* 3.5 12.3 - - + -
53U CYS* 3.8 2.2 - - - -
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Residues in contact with THR 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40U GLU* 3.0 25.7 + - - +
41U LYS* 3.8 4.9 - - + +
43U MET* 1.3 77.5 - - - +
45U ALA* 1.3 62.0 + - - +
46U LYS 3.4 1.1 + - - -
47U GLY* 3.7 9.1 + - - -
48U GLY 4.9 0.7 - - - +
50U VAL* 3.6 15.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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