Contacts of the helix formed by residues 35 - 55 (chain B) in PDB entry 1Q90
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 2.9 35.0 + - - +
34B TYR* 1.3 77.2 - - - +
36B ILE* 1.3 60.3 + - - +
37B GLY 3.3 1.6 - - - -
38B GLY* 3.1 5.9 + - - -
39B ILE* 2.9 32.2 + - + +
903B HEC 1.8 68.8 - - + +
904B BCR 4.4 12.3 - - + -
43D VAL* 4.5 5.8 - - + -
91N VAL* 5.1 0.4 - - - -
95N ARG* 5.1 0.4 - - - -
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE 4.7 2.0 - - - +
33B PHE* 3.3 41.9 + - + +
35B CYS* 1.3 76.9 - - - +
37B GLY* 1.3 66.2 + - - +
39B ILE* 3.6 16.5 - - + +
40B THR* 2.9 26.7 + - - -
96B MET* 3.3 32.5 - - + +
99B LEU* 3.9 28.3 - - + +
100B HIS* 3.3 19.5 - - + +
103B ARG* 5.2 1.3 - - + -
904B BCR 5.0 14.8 - - + -
17G THR* 4.5 6.5 - - + -
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 1.3 76.9 - - - +
38B GLY* 1.3 58.0 + - - +
40B THR* 3.1 8.6 - - - -
41B PHE* 3.0 21.1 + - - +
100B HIS* 3.6 21.4 + - - -
901B HEC 3.1 45.4 + - - +
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Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B CYS* 3.1 7.1 + - - +
37B GLY* 1.3 74.1 - - - +
39B ILE* 1.3 55.4 + - - +
41B PHE* 3.2 4.7 + - - +
42B THR* 2.7 38.4 + - - -
901B HEC 3.5 8.1 + - - +
903B HEC 3.4 41.1 + - - +
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Residues in contact with ILE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B CYS 2.9 20.4 + - - +
36B ILE* 3.2 17.5 + - + +
38B GLY* 1.3 75.2 - - - +
40B THR* 1.3 65.8 + - - +
42B THR* 2.9 11.0 + - - -
43B CYS* 2.8 21.2 + - - +
96B MET* 4.0 13.0 - - + -
903B HEC 4.5 1.3 - - - +
904B BCR 3.6 51.1 - - + -
43D VAL* 3.7 20.2 - - + -
47D THR* 3.6 9.6 - - + +
951L LMG 3.5 31.6 - - + -
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 2.9 15.3 + - - +
37B GLY* 3.1 11.1 - - - -
39B ILE* 1.3 77.0 - - - +
41B PHE* 1.3 63.1 + - - -
43B CYS* 2.9 17.7 + - - +
44B PHE* 2.9 11.8 + - - +
93B MET* 3.9 27.4 - - + +
96B MET* 3.4 29.2 + - - +
97B MET* 3.6 7.5 + - + -
100B HIS* 4.3 1.4 - - - +
901B HEC 3.5 35.2 - - + -
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY 3.0 12.6 + - - +
38B GLY* 3.4 10.5 - - - +
40B THR* 1.3 75.3 - - - +
42B THR* 1.3 63.1 + - - +
44B PHE* 2.9 21.7 + + - +
45B LEU* 2.9 49.3 + - + +
199B MET* 3.9 22.4 - - + -
203B PHE* 3.7 39.0 - + + -
901B HEC 3.5 11.3 - - + +
903B HEC 3.7 33.0 - - + -
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Residues in contact with THR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLY 2.7 26.3 + - - -
39B ILE* 3.1 13.9 - - - -
41B PHE* 1.3 73.5 - - - +
43B CYS* 1.3 56.1 + - - +
45B LEU* 3.3 11.0 + - + +
46B VAL* 2.9 32.0 + - + +
903B HEC 3.7 22.1 - - + +
43D VAL* 5.9 0.2 - - - +
44D ILE* 4.0 21.6 - - + +
47D THR* 4.2 15.5 - - + -
48D PHE* 3.9 25.8 - - + -
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Residues in contact with CYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE 2.8 10.7 + - - -
40B THR 3.2 9.4 - - - +
42B THR* 1.3 73.5 - - - +
44B PHE* 1.3 61.3 + - - +
46B VAL* 3.3 6.3 + - - +
47B GLN* 2.9 33.5 + - - +
89B SER* 3.4 14.3 + - - +
92B MET* 3.9 19.3 - - - -
93B MET* 3.8 22.2 - - + -
96B MET* 4.6 3.1 - - - -
47D THR* 4.7 4.3 - - - -
51D VAL* 5.3 2.0 - - - -
951L LMG 3.4 33.4 - - - -
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B THR 2.9 7.1 + - - +
41B PHE* 2.9 18.9 + + - +
43B CYS* 1.3 75.1 - - - +
45B LEU* 1.3 65.7 - - + +
47B GLN* 3.0 6.9 + - - +
48B VAL* 2.9 51.8 + - + +
93B MET* 3.8 28.0 - - + -
131B PHE* 3.9 21.3 - + - -
192B PRO* 4.8 10.1 - - + -
195B THR* 3.7 25.6 - - + -
196B ALA* 4.9 7.9 - - + -
199B MET* 3.6 30.1 - - + -
902B HEC 3.9 18.6 - - + -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 2.9 54.4 + - + +
42B THR* 3.6 12.3 - - + +
44B PHE* 1.3 77.0 - - + +
46B VAL* 1.3 66.5 + - - +
48B VAL* 3.1 15.9 + - + +
49B ALA* 3.1 23.4 + - - +
903B HEC 5.6 4.7 - - + -
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR* 2.9 24.3 + - + +
43B CYS* 3.4 9.4 - - - +
44B PHE 3.2 0.2 - - - -
45B LEU* 1.3 76.0 - - + +
47B GLN* 1.3 65.0 + - - +
49B ALA* 3.3 4.4 + - - +
50B THR* 2.9 28.9 + - + +
85B ILE* 3.8 26.2 - - + -
89B SER* 3.7 15.9 - - - +
960B LFA 4.0 17.0 - - + +
47D THR* 5.7 2.2 - - + -
48D PHE* 3.5 35.7 - - + -
51D VAL* 5.5 2.0 - - + -
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B CYS 2.9 19.5 + - - +
44B PHE* 3.2 9.0 - - - +
46B VAL* 1.3 77.8 - - - +
48B VAL* 1.3 52.3 + - - +
50B THR* 3.1 4.4 - - - +
51B GLY* 2.6 35.0 + - - -
86B HIS* 3.0 47.6 + - - +
89B SER* 2.7 38.7 + - - +
90B ALA* 3.1 8.4 - - - +
93B MET* 4.9 0.9 - - - -
902B HEC 3.4 49.1 - - + -
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PHE* 2.9 53.8 + - + +
45B LEU* 3.1 15.2 + - + +
47B GLN* 1.3 76.5 - - - +
49B ALA* 1.3 55.6 + - - +
52B PHE* 2.7 40.9 + - + +
902B HEC 3.8 26.0 - - + +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU 3.1 8.8 + - - +
46B VAL* 3.7 8.1 - - - +
48B VAL* 1.3 78.9 - - - +
50B THR* 1.3 58.5 + - - +
52B PHE* 3.4 4.2 + - - +
53B ALA* 3.0 20.3 + - - +
960B LFA 5.4 8.3 - - + -
64R TYR* 2.8 36.4 + - + +
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Residues in contact with THR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 2.9 33.8 + - + +
47B GLN* 3.1 10.1 - - - +
49B ALA* 1.3 74.2 - - - +
51B GLY* 1.3 62.3 + - - +
53B ALA* 3.5 7.0 - - - +
54B MET* 3.5 23.0 + - - +
82B ILE* 3.3 37.7 + - - +
85B ILE* 4.0 6.3 - - - +
86B HIS* 2.7 45.7 + - + +
960B LFA 5.3 5.5 - - - +
64R TYR* 4.6 4.0 - - - -
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Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN 2.6 17.6 + - - -
48B VAL 3.5 0.2 - - - -
50B THR* 1.3 70.0 - - - +
52B PHE* 1.3 66.4 + - - +
53B ALA 3.0 1.6 - - - -
54B MET* 2.9 15.5 + - - +
55B THR* 3.3 8.8 + - - -
86B HIS* 3.2 25.1 - - - -
902B HEC 3.4 24.5 - - - +
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B VAL* 2.7 25.0 + - + +
49B ALA* 3.7 2.7 - - - +
51B GLY* 1.3 71.2 - - - -
53B ALA* 1.3 60.4 + - - +
55B THR* 2.9 38.3 + - + -
56B PHE* 3.7 34.1 + + - -
902B HEC 3.4 10.8 - - + +
64R TYR* 3.5 16.4 - + - -
68R PHE* 3.5 24.9 - + - -
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ALA 3.0 17.5 + - - +
50B THR 3.5 8.1 - - - +
51B GLY 3.0 0.4 + - - -
52B PHE* 1.3 78.1 - - - +
54B MET* 1.3 61.3 + - - +
55B THR 3.1 1.0 + - - -
56B PHE* 3.2 13.7 + - - +
82B ILE* 4.4 5.4 - - + -
64R TYR* 3.8 19.1 - - + +
67R PHE* 3.0 35.9 - - + -
68R PHE* 3.8 17.5 - - + -
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Residues in contact with MET 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B THR 3.6 13.9 - - - +
51B GLY 2.9 9.0 + - - +
53B ALA* 1.3 72.0 - - - +
55B THR* 1.3 57.3 + - - +
56B PHE 3.0 5.6 - - - -
57B TYR* 3.0 3.2 + - - +
58B TYR* 2.9 30.0 + - - +
72B ILE* 3.7 31.0 - - + -
82B ILE* 4.0 10.3 - - + -
83B ARG* 3.3 38.1 - - + +
86B HIS* 4.5 12.8 - - - -
902B HEC 3.1 55.9 - - + +
67R PHE* 4.1 7.6 - - + -
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLY 3.3 9.8 + - - -
52B PHE* 2.9 30.3 + - + -
54B MET* 1.3 78.6 - - - +
56B PHE* 1.3 63.4 + - + +
57B TYR 3.2 1.9 + - - -
58B TYR* 4.5 8.7 + - - +
184B TYR* 3.5 26.8 + - + +
188B THR* 4.7 2.4 - - + +
902B HEC 3.9 13.3 - - - +
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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