Contacts of the helix formed by residues 30 - 48 (chain B) in PDB entry 1QM4
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 HIS 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 3.6 33.4 - - + +
27B GLY 3.1 15.5 + - - +
29B GLY* 1.3 74.9 - - - +
31B PRO* 1.3 66.2 - - + +
32B ASP* 3.3 29.5 + - + +
33B LYS* 3.1 6.6 + - + -
34B ILE 2.8 30.5 + - - -
180B ASP* 3.0 20.6 + - - +
181B SER 4.3 3.8 - - - +
182B LYS* 5.5 6.7 - - + +
266B LYS* 3.3 32.1 + - - -
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Residues in contact with PRO 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLY 3.1 4.4 - - - +
30B HIS* 1.3 96.8 - - + +
32B ASP* 1.3 62.1 + - - +
34B ILE* 3.2 6.3 + - + +
35B CYS* 3.2 26.9 + - - -
61B CYS* 3.6 3.2 - - - -
180B ASP* 4.2 9.4 - - - +
256B PRO* 3.4 35.2 - - + -
257B GLN 3.9 8.5 - - - +
258B GLY* 4.0 14.8 - - - +
260B ALA 4.7 0.7 - - - -
261B GLY* 3.5 24.2 - - - +
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A SO4 5.0 0.2 + - - -
30B HIS* 3.3 16.7 + - + +
31B PRO* 1.3 76.0 - - - +
33B LYS* 1.3 58.1 + - - +
35B CYS 3.1 1.9 + - - -
36B ASP* 3.0 28.2 + - - +
261B GLY* 3.5 2.8 - - - -
262B VAL 3.0 39.7 + - - +
265B ARG* 3.0 39.0 + - + +
266B LYS* 3.4 38.5 + - + +
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 3.3 24.7 - - + -
27B GLY 3.7 14.4 - - - +
28B GLU 4.7 0.2 - - - +
30B HIS* 3.1 9.3 + - - +
32B ASP* 1.3 74.9 - - - +
34B ILE* 1.3 66.8 + - - +
36B ASP* 3.1 23.1 + - - +
37B GLN* 3.1 33.0 + - - +
266B LYS* 3.8 14.4 - - + -
269B VAL* 3.6 22.7 - - - -
270B ASP* 2.9 28.4 + - - -
376B ALA* 3.0 28.6 + - - +
377B CYS* 4.0 18.2 - - - +
378B TYR 5.3 1.3 - - - +
379B GLY 5.9 0.2 - - - +
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU 3.7 16.6 - - - +
29B GLY* 3.4 8.1 - - - +
30B HIS 2.8 16.1 + - - +
31B PRO* 3.4 7.2 - - + +
32B ASP 3.2 0.6 - - - -
33B LYS* 1.3 76.4 - - - +
35B CYS* 1.3 57.6 + - - +
37B GLN* 3.7 4.1 - - - +
38B ILE* 3.0 46.0 + - + +
61B CYS* 4.5 11.4 - - + -
88B ILE* 4.9 7.2 - - + -
91B ILE* 4.1 16.3 - - + +
93B TYR* 3.8 11.2 - - + -
100B PHE* 4.3 8.1 - - + -
256B PRO* 2.9 44.6 - - + -
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Residues in contact with CYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PRO 3.4 13.0 - - - -
32B ASP 3.1 10.0 + - - +
34B ILE* 1.3 78.1 - - - +
36B ASP* 1.3 62.2 + - - +
38B ILE 4.5 0.2 - - - +
39B SER* 2.8 31.0 + - - -
59B THR* 3.5 29.0 + - - +
60B VAL 3.9 0.9 - - - -
61B CYS* 3.5 27.4 - - - -
261B GLY 3.5 15.9 - - - -
262B VAL 3.5 6.7 - - - -
263B THR* 3.5 16.6 - - - +
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP 3.0 20.7 + - - +
33B LYS* 3.1 29.7 + - - +
35B CYS* 1.3 75.4 - - - +
37B GLN* 1.3 62.6 + - - +
39B SER* 3.8 0.2 - - - -
40B ASP 3.2 15.9 + - - -
262B VAL 4.8 0.5 - - - +
263B THR* 3.3 7.3 - - - +
264B GLY* 3.1 29.3 + - - -
265B ARG 5.0 0.2 + - - -
266B LYS* 4.2 9.7 + - - +
270B ASP* 4.4 6.3 - - - +
284B SER* 3.4 32.6 + - - +
376B ALA* 3.6 16.7 - - - +
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Residues in contact with GLN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU* 2.9 47.5 + - - +
33B LYS 3.1 21.1 + - - +
34B ILE 3.7 3.4 - - - +
36B ASP* 1.3 74.1 - - - +
38B ILE* 1.3 60.8 + - - +
40B ASP* 3.2 2.8 + - - +
41B ALA* 2.8 29.6 + - - +
87B THR* 4.1 12.1 - - + -
90B HIS* 4.5 4.9 + - - -
91B ILE* 3.9 18.4 - - + +
373B GLN* 4.0 24.1 + - + +
376B ALA* 3.6 27.1 - - + +
377B CYS* 3.9 12.8 - - - +
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 3.0 38.5 + - + +
35B CYS 4.0 0.9 - - - +
37B GLN* 1.3 75.2 - - - +
39B SER* 1.3 57.3 + - - +
41B ALA* 3.2 3.7 + - - +
42B VAL* 3.0 32.0 + - + +
59B THR* 3.7 24.0 - - + +
61B CYS* 5.9 0.2 - - + -
66B VAL* 3.7 26.7 - - + -
68B LEU* 5.1 1.6 - - + -
83B VAL 5.1 0.9 - - - +
84B VAL* 3.8 37.0 - - + +
87B THR* 4.1 21.8 - - + -
88B ILE* 4.3 10.5 - - + -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B CYS 2.8 16.6 + - - -
36B ASP 3.8 4.7 - - - -
38B ILE* 1.3 78.0 - - - +
40B ASP* 1.3 57.5 + - - +
42B VAL* 3.5 1.5 + - - -
43B LEU* 3.2 21.1 + - - +
57B CYS* 3.5 24.5 - - - -
58B GLU* 3.6 1.9 - - - -
59B THR* 2.8 26.5 + - - -
263B THR* 3.3 16.9 + - - -
285B GLY* 3.9 22.8 - - - -
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Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ASP 3.2 7.0 + - - +
37B GLN 3.2 2.5 + - - +
39B SER* 1.3 76.7 - - - +
41B ALA* 1.3 60.1 + - - +
42B VAL 3.2 0.4 - - - -
43B LEU* 3.2 5.9 + - - +
44B ASP* 2.9 32.6 + - - +
284B SER* 2.8 27.3 + - - -
285B GLY 3.2 9.5 + - - -
293B ARG* 2.8 42.5 + - - -
372B TYR* 3.3 28.1 - - - +
373B GLN* 3.7 8.1 - - - +
375B THR* 3.8 0.2 - - - +
376B ALA* 3.4 6.2 - - + +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLN 2.8 15.6 + - - +
38B ILE 3.2 5.6 + - - +
40B ASP* 1.3 76.2 - - - +
42B VAL* 1.3 59.3 + - - +
44B ASP* 3.3 4.3 + - - +
45B ALA* 2.9 30.5 + - - +
83B VAL* 4.2 10.9 - - + +
87B THR* 3.2 26.9 - - - +
373B GLN* 3.5 21.1 - - - +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 3.0 20.2 + - + +
39B SER 3.8 8.1 - - - +
40B ASP 3.2 0.2 - - - -
41B ALA* 1.3 79.5 - - - +
43B LEU* 1.3 58.3 + - - +
45B ALA* 3.7 2.4 + - - +
46B HIS* 3.1 25.2 + - + -
55B VAL* 5.2 0.7 - - + -
57B CYS* 4.1 13.7 - - + -
68B LEU* 4.2 18.6 - - + -
72B ILE* 4.1 15.3 - - + -
78B ILE* 5.6 0.2 - - + -
80B TYR* 3.5 35.4 - - + -
83B VAL* 3.5 25.1 - - + -
84B VAL* 4.9 1.1 - - + -
111B LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 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 SER 3.2 14.3 + - - +
40B ASP* 3.5 10.5 - - - +
41B ALA 3.2 0.4 - - - -
42B VAL* 1.3 75.0 - - - +
44B ASP* 1.3 64.6 + - - +
46B HIS* 3.2 2.9 + - - +
47B LEU* 3.0 36.0 + - + +
55B VAL* 3.6 37.2 - - + +
285B GLY* 5.4 0.4 - - - -
286B LYS 3.4 27.8 - - - +
287B ASP* 3.8 14.6 - - + -
293B ARG* 3.6 11.2 - - - +
372B TYR* 3.4 33.4 - - + -
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Residues in contact with ASP 44 (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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40B ASP 2.9 15.2 + - - +
41B ALA* 3.6 6.3 - - - +
43B LEU* 1.3 73.8 - - - +
45B ALA* 1.3 64.0 + - - +
46B HIS 2.9 2.1 + - - -
47B LEU* 3.0 11.3 + - - +
48B LYS* 3.1 25.0 + - - +
370B PRO* 3.4 34.7 - - + +
371B ILE 4.2 0.3 - - - -
372B TYR* 3.2 26.9 + - - +
373B GLN* 3.0 31.1 + - - +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA 2.9 17.0 + - - +
42B VAL 3.7 7.2 - - - +
43B LEU 3.4 0.2 - - - -
44B ASP* 1.3 76.0 - - - +
46B HIS* 1.3 57.9 + - - +
48B LYS* 4.4 13.4 + - - +
49B GLN* 4.3 11.8 + - - +
78B ILE* 3.5 30.9 - - + +
83B VAL* 4.1 21.3 - - + -
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Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.1 25.4 + - + +
43B LEU 3.2 7.0 + - - +
44B ASP 3.1 0.8 - - - -
45B ALA* 1.3 74.8 - - - +
47B LEU* 1.3 63.5 + - + +
48B LYS 3.2 1.8 - - - -
49B GLN* 3.0 4.3 + - - +
50B ASP* 2.8 31.9 + - - +
53B ALA* 3.7 13.7 - - + +
55B VAL* 4.1 9.4 - - + +
72B ILE* 3.2 21.7 - - + +
74B SER* 2.9 27.4 + - - -
76B ALA* 4.4 0.8 - - - +
78B ILE* 3.7 24.5 - - + +
80B TYR* 3.0 31.3 + - - -
113B GLN* 3.7 19.3 - - - -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.0 34.9 + - + +
44B ASP 3.0 4.5 + - - +
46B HIS* 1.3 77.7 - - - +
48B LYS* 1.3 62.1 + - - +
49B GLN 3.1 1.4 + - - -
50B ASP 3.3 20.1 + - - +
51B PRO* 3.3 22.3 - - + +
53B ALA* 4.4 10.5 - - + +
288B TYR* 4.1 22.4 - - + -
368B LYS* 3.3 28.3 - - - +
369B LYS 4.1 4.0 - - - +
370B PRO* 4.2 11.0 - - + -
372B TYR* 3.6 37.7 - - + -
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Residues in contact with LYS 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 ASP* 3.1 22.7 + - - +
45B ALA* 4.5 10.1 - - - +
46B HIS 3.2 0.2 - - - -
47B LEU* 1.3 77.1 - - - +
49B GLN* 1.3 63.2 + - + +
51B PRO* 5.5 0.7 - - - -
370B PRO* 3.8 31.2 - - + +
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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
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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