Contacts of the helix formed by residues 35 - 54 (chain N) in PDB entry 2D2C
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 CYS 35 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N PHE* 2.5 29.6 + - - +
34N TYR* 1.3 73.2 - - - +
36N LEU* 1.3 54.7 + - - +
37N GLY 2.6 17.6 + - - -
38N GLY* 2.6 19.1 + - - -
39N ILE* 2.8 27.1 + - + -
302N HEM 3.7 3.9 - - - +
303N HEC 1.8 63.9 - - + -
43O VAL* 4.7 0.2 - - - -
1101R BCR 4.4 11.6 - - + +
23T GLN* 4.9 2.7 - - - -
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Residues in contact with LEU 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N PHE* 4.4 12.1 - - + -
34N TYR* 3.4 22.6 - - - +
35N CYS* 1.3 75.9 - - - +
37N GLY* 1.3 51.8 + - - +
39N ILE* 3.8 8.6 - - + +
40N THR* 2.4 43.7 + - - -
96N MET* 3.4 30.5 - - - +
99N LEU* 3.5 28.0 - - + +
100N HIS* 3.4 31.6 - - + +
103N ARG* 4.8 10.5 - - + +
14R LEU* 4.9 7.2 - - + -
1101R BCR 5.0 11.6 - - + +
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Residues in contact with GLY 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N CYS 2.6 6.9 + - - -
36N LEU* 1.3 76.8 - - - +
38N GLY* 1.3 61.8 + - - -
40N THR* 3.4 1.6 - - - -
41N LEU 3.1 14.6 + - - -
100N HIS* 3.1 35.7 + - - -
103N ARG* 4.6 0.2 - - - +
302N HEM 3.0 32.4 - - - +
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Residues in contact with GLY 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N CYS 2.6 10.1 + - - -
37N GLY* 1.3 71.6 - - - -
39N ILE* 1.3 48.3 + - - -
41N LEU* 3.1 8.5 - - - +
42N THR* 2.8 34.5 + - - -
302N HEM 3.0 18.1 + - - +
303N HEC 3.1 40.1 - - - -
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Residues in contact with ILE 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N CYS* 2.8 31.1 + - + +
36N LEU* 3.6 11.4 - - + +
38N GLY* 1.3 72.2 - - - +
40N THR* 1.3 71.9 + - - +
42N THR* 2.9 22.1 + - - +
43N CYS* 3.2 9.7 - - - -
96N MET* 3.6 40.6 - - + -
303N HEC 4.1 8.9 - - + -
43O VAL* 3.2 35.0 - - + -
47O THR* 3.8 17.9 - - + +
1101R BCR 3.6 13.2 - - + -
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Residues in contact with THR 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N LEU 2.4 32.8 + - - -
37N GLY* 3.4 4.9 - - - -
39N ILE* 1.3 74.1 - - - +
41N LEU* 1.3 69.5 + - - +
43N CYS* 3.2 4.3 + - - +
93N MET* 3.0 35.3 - - + +
96N MET* 3.1 27.5 + - - -
97N MET* 3.2 31.0 - - + -
100N HIS* 3.9 2.6 - - - +
302N HEM 3.9 23.8 - - + -
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Residues in contact with LEU 41 (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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37N GLY 3.1 5.9 + - - +
38N GLY* 3.1 8.5 - - - +
40N THR* 1.3 77.9 - - - +
42N THR* 1.3 71.3 - - - +
44N PHE* 2.4 42.3 + - + +
45N LEU* 3.2 26.1 + - + -
93N MET* 4.8 0.2 - - - -
199N MET* 3.8 11.2 - - + -
203N PHE* 3.4 32.8 - - + -
302N HEM 3.3 20.9 - - + +
303N HEC 3.6 37.7 - - + -
1305N OPC 3.7 7.9 - - - +
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Residues in contact with THR 42 (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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38N GLY 2.8 22.1 + - - -
39N ILE* 2.9 18.6 + - - +
41N LEU* 1.3 77.5 - - - +
43N CYS* 1.3 58.2 + - - +
44N PHE 2.5 13.7 + - - -
45N LEU* 2.7 22.0 + - - +
46N ILE* 3.4 19.5 + - + -
303N HEC 3.6 20.4 - - + +
1305N OPC 3.7 8.0 + - - +
44O ILE* 4.4 29.4 - - + +
47O THR* 5.1 6.7 - - - +
48O PHE* 6.3 0.2 - - + -
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Residues in contact with CYS 43 (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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39N ILE* 3.2 22.9 - - - -
40N THR 3.2 3.1 + - - +
41N LEU 3.1 0.2 + - - -
42N THR* 1.3 80.3 - - - +
44N PHE* 1.3 61.8 + - - +
46N ILE* 3.1 13.5 - - + +
47N GLN* 3.1 14.6 + - - +
89N SER* 2.9 32.7 + - - +
92N MET* 5.0 3.6 - - - -
93N MET* 3.5 34.1 - - + -
96N MET* 4.3 13.2 - - - -
47O THR* 5.3 7.9 - - - -
51O ILE* 6.0 3.6 - - + -
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Residues in contact with PHE 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N LEU* 2.4 29.3 + - + +
42N THR 2.5 0.2 + - - -
43N CYS* 1.3 68.2 - - - +
45N LEU* 1.3 65.2 + - + -
46N ILE 2.7 4.0 - - - -
47N GLN* 2.3 29.0 + - - +
48N PHE* 2.6 53.8 + + + -
93N MET* 3.3 17.2 - - + -
131N PHE* 4.7 5.2 - + - -
192N PRO* 5.3 5.8 - - + -
195N ILE* 3.8 39.9 - - + -
196N ALA* 6.2 2.0 - - + -
199N MET* 4.9 15.0 - - + -
301N HEM 3.4 31.4 - - + -
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Residues in contact with LEU 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N LEU* 3.2 28.5 - - + -
42N THR* 2.7 12.5 + - - +
44N PHE* 1.3 86.5 - - + +
46N ILE* 1.3 58.6 + - - +
48N PHE* 3.8 12.6 - - + +
49N ALA* 3.4 20.6 + - - +
303N HEC 5.4 0.7 - - + -
1305N OPC 2.7 78.7 + - - +
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Residues in contact with ILE 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42N THR* 4.0 13.7 - - + +
43N CYS* 3.1 27.4 - - + +
44N PHE 2.6 0.4 + - - -
45N LEU* 1.3 80.8 - - - +
47N GLN* 1.3 49.0 + - - -
49N ALA* 3.7 1.7 - - - +
50N THR* 2.7 44.3 + - + +
85N ILE* 3.4 28.7 - - + -
89N SER* 3.0 20.9 - - - +
1305N OPC 4.0 22.7 - - - +
47O THR 4.7 12.3 - - - +
48O PHE* 4.8 24.5 - - + -
51O ILE* 5.0 5.4 - - + -
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Residues in contact with GLN 47 (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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43N CYS 3.1 6.1 + - - +
44N PHE 2.3 24.4 + - - +
46N ILE* 1.3 67.2 - - - +
48N PHE* 1.3 56.5 + - - -
49N ALA 3.1 1.6 - - - -
50N THR* 2.9 7.7 + - - -
51N GLY* 2.6 31.0 + - - -
86N HIS* 2.6 57.6 + - + -
89N SER* 2.8 18.8 + - - -
90N ALA* 2.4 39.4 - - - +
93N MET* 5.6 0.4 - - - +
301N HEM 3.1 45.1 - - + +
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Residues in contact with PHE 48 (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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189A PHE* 3.9 27.6 - + - -
193A TRP* 4.3 35.9 - + + -
44N PHE* 2.6 48.2 + + + +
45N LEU* 4.0 11.7 - - + -
47N GLN* 1.3 73.3 - - - +
49N ALA* 1.3 63.0 + - + +
52N PHE* 2.9 37.2 + + + +
192N PRO* 5.8 1.6 - - + -
301N HEM 3.6 17.6 - - + +
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Residues in contact with ALA 49 (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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45N LEU 3.4 18.3 + - - +
46N ILE* 3.7 4.0 - - - +
47N GLN 3.1 0.6 - - - -
48N PHE* 1.3 81.3 - - + +
50N THR* 1.3 72.5 + - + +
51N GLY 3.0 0.2 - - - -
52N PHE* 2.6 12.0 + - - -
53N ALA* 2.6 25.7 + - - -
1305N OPC 5.0 19.5 - - - -
38Q LEU* 5.6 8.1 - - + -
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Residues in contact with THR 50 (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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46N ILE* 2.7 27.7 + - + +
47N GLN* 2.9 2.9 + - - -
49N ALA* 1.3 77.9 - - + +
51N GLY* 1.3 80.0 + - - +
53N ALA* 3.1 15.2 + - - +
54N MET* 3.2 13.9 + - - +
82N ILE* 3.5 30.2 - - + +
85N ILE* 3.8 31.9 - - + -
86N HIS* 2.6 26.1 + - - -
1305N OPC 6.5 0.9 - - - -
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Residues in contact with GLY 51 (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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47N GLN 2.6 18.6 + - - -
49N ALA 2.7 0.6 + - - -
50N THR* 1.3 86.0 + - - +
52N PHE* 1.3 62.4 + - - +
54N MET* 2.7 32.0 + - - +
55N THR 3.7 0.7 + - - -
86N HIS* 3.4 2.9 - - - -
301N HEM 3.3 26.1 - - - +
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Residues in contact with PHE 52 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER* 3.9 3.1 - - - -
189A PHE* 3.1 36.8 - + + -
190A VAL* 3.9 14.6 - - + -
48N PHE* 2.9 26.5 + + + +
49N ALA* 2.6 10.8 + - - -
51N GLY* 1.3 64.6 - - - -
53N ALA* 1.3 58.2 - - + +
54N MET 2.3 20.8 + - - -
55N THR* 2.4 29.8 + - - +
56N PHE* 3.5 35.4 + + - -
301N HEM 3.0 15.4 - - - +
42Q PHE* 3.7 23.8 - + - -
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Residues in contact with ALA 53 (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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49N ALA 2.6 15.1 + - - +
50N THR* 3.1 19.5 - - - +
52N PHE* 1.3 73.4 - - + +
54N MET* 1.3 52.2 + - - +
56N PHE* 3.8 10.4 - - - +
82N ILE* 4.3 7.6 - - + -
38Q LEU* 4.5 11.9 - - + -
41Q TYR* 2.4 39.5 + - + +
42Q PHE* 3.7 28.3 - - + -
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Residues in contact with MET 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N THR* 3.2 21.5 - - - +
51N GLY* 2.7 27.0 + - - +
52N PHE 2.3 13.7 + - - -
53N ALA* 1.3 69.7 - - - +
55N THR* 1.3 52.6 + - - -
56N PHE 2.6 16.8 + - - -
57N TYR* 2.8 13.4 + - - +
58N TYR* 2.9 15.8 + - + +
72N ILE* 5.7 14.6 - - + -
82N ILE* 4.1 11.7 - - + -
83N ARG* 4.6 13.7 - - - -
86N HIS* 3.4 34.1 - - + +
301N HEM 3.7 38.4 - - + +
41Q TYR* 3.5 11.2 - - + +
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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