Contacts of the helix formed by residues 30 - 48 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.6 32.0 - - + +
27A GLY 3.1 15.3 + - - +
29A GLY* 1.3 77.2 - - - +
31A PRO* 1.3 66.6 - - + +
32A ASP* 3.4 28.2 + - + +
33A LYS* 3.0 6.8 + - + -
34A ILE* 2.8 30.7 + - - +
180A ASP* 3.1 14.4 + - - +
181A SER 4.3 2.7 - - - +
182A LYS* 5.4 2.8 - - + +
266A LYS* 3.3 33.2 + - - -
401A AMB 3.7 23.7 + - - -
404A MG 4.3 0.9 - - - -
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Residues in contact with PRO 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY 3.1 4.4 - - - +
30A HIS* 1.3 93.6 - - + +
32A ASP* 1.3 62.1 + - - +
34A ILE* 3.1 13.6 + - + +
35A CYS* 3.1 19.4 + - - -
61A CYS* 3.7 3.7 - - - -
180A ASP* 4.2 0.2 - - - +
256A PRO* 3.3 35.2 - - + -
257A GLN 3.5 10.1 - - - +
258A GLY* 4.1 11.0 - - - +
260A ALA 4.1 4.5 - - - +
261A GLY* 3.4 24.4 - - - +
404A MG 3.6 17.7 - - - -
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 3.3 15.7 + - - +
31A PRO* 1.3 77.7 - - - +
33A LYS* 1.3 58.9 + - - +
35A CYS 3.2 1.7 + - - -
36A ASP* 3.0 28.6 + - - +
260A ALA 4.1 1.2 - - - +
261A GLY* 3.5 2.4 - - - -
262A VAL 2.9 40.3 + - - +
265A ARG* 3.1 38.2 + - + +
266A LYS* 3.3 39.9 + - + +
401B SO4 4.2 0.2 + - - -
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.4 25.4 - - + -
27A GLY 3.7 14.4 - - - +
28A GLU 4.8 0.2 - - - +
30A HIS* 3.0 10.4 + - - +
32A ASP* 1.3 76.6 - - - +
34A ILE* 1.3 65.4 + - - +
36A ASP* 3.1 22.2 + - - +
37A GLN* 3.1 33.9 + - - +
266A LYS* 3.9 12.8 - - + -
269A VAL* 3.6 21.5 - - - -
270A ASP* 2.8 29.3 + - - -
284A SER* 5.6 0.2 + - - -
376A ALA* 3.0 26.5 + - - +
377A CYS* 4.0 18.4 - - - +
378A TYR 5.2 2.2 - - - +
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU 3.7 14.6 - - - +
29A GLY* 3.5 6.1 - - - +
30A HIS 2.8 16.3 + - - +
31A PRO* 3.1 8.5 + - + +
33A LYS* 1.3 79.4 - - - +
35A CYS* 1.3 56.6 + - - +
37A GLN* 3.4 4.5 + - - +
38A ILE* 3.0 45.9 + - + +
61A CYS* 4.4 10.3 - - + -
66A VAL* 5.7 0.2 - - + -
88A ILE* 4.9 7.2 - - + -
91A ILE* 4.2 14.4 - - + +
93A TYR* 3.9 9.6 - - + -
100A PHE* 4.3 10.1 - - + -
256A PRO* 3.0 46.7 - - + -
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Residues in contact with CYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO 3.1 12.2 + - - -
32A ASP 3.3 9.2 - - - +
34A ILE* 1.3 78.3 - - - +
36A ASP* 1.3 61.6 + - - +
37A GLN 3.2 0.2 - - - -
38A ILE 4.6 0.2 - - - +
39A SER* 2.8 31.5 + - - -
59A THR* 3.6 20.7 + - - +
60A VAL 3.8 2.5 - - - -
61A CYS* 3.5 24.7 - - - -
261A GLY 3.4 26.7 - - - -
262A VAL 3.5 7.9 - - - -
263A THR* 3.5 17.0 - - - +
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP* 3.0 19.7 + - - +
33A LYS* 3.1 26.7 + - - +
34A ILE 3.4 0.2 - - - -
35A CYS* 1.3 76.0 - - - +
37A GLN* 1.3 60.9 + - - +
39A SER 3.7 0.2 + - - -
40A ASP 3.2 16.1 + - - -
262A VAL 4.8 0.3 - - - +
263A THR* 3.4 7.0 - - - +
264A GLY* 3.1 29.8 + - - -
265A ARG 5.1 0.2 + - - -
266A LYS* 4.3 9.2 + - - +
270A ASP* 4.5 7.3 - - - +
284A SER* 3.4 32.7 + - - +
376A ALA* 3.4 19.8 - - - +
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Residues in contact with GLN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.0 47.0 + - - +
33A LYS 3.1 18.3 + - - +
34A ILE 3.7 3.6 - - - +
36A ASP* 1.3 76.0 - - - +
38A ILE* 1.3 60.5 + - - +
40A ASP* 3.1 3.3 + - - +
41A ALA* 2.8 29.3 + - - +
87A THR* 4.1 12.3 - - + -
90A HIS* 4.5 5.5 + - - -
91A ILE* 3.8 17.5 - - + +
373A GLN* 4.1 23.8 + - + +
376A ALA* 3.6 26.0 - - + +
377A CYS* 4.0 12.2 - - - +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.0 34.4 + - + +
35A CYS 4.1 0.4 - - - +
37A GLN* 1.3 75.0 - - - +
39A SER* 1.3 62.9 + - - +
41A ALA* 3.2 4.0 + - - +
42A VAL* 3.0 26.6 + - + +
59A THR* 3.7 24.7 - - + +
61A CYS* 5.9 0.2 - - + -
66A VAL* 3.8 27.1 - - + -
68A LEU* 5.0 2.2 - - + -
83A VAL 5.2 0.7 - - - +
84A VAL* 3.8 35.9 - - + +
87A THR* 4.0 22.6 - - + +
88A ILE* 4.3 9.9 - - + -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS 2.8 21.8 + - - -
36A ASP 3.8 4.9 - - - -
38A ILE* 1.3 76.0 - - - +
40A ASP* 1.3 59.4 + - - +
42A VAL* 3.5 1.5 + - - -
43A LEU* 3.2 21.5 + - - +
57A CYS* 3.6 22.8 - - - -
58A GLU* 3.6 1.7 - - - -
59A THR* 2.9 20.4 + - - -
263A THR* 3.3 17.6 + - - +
285A GLY* 3.9 24.0 - - - -
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Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP 3.2 6.8 + - - +
37A GLN 3.1 2.3 + - - +
39A SER* 1.3 77.3 - - - +
41A ALA* 1.3 60.7 + - - +
42A VAL 3.2 0.4 - - - -
43A LEU* 3.6 6.6 - - - +
44A ASP* 2.9 32.1 + - - +
284A SER* 2.7 29.0 + - - -
285A GLY 3.1 9.7 + - - -
293A ARG* 2.8 40.6 + - - -
372A TYR* 3.4 27.5 - - + +
373A GLN* 3.7 7.9 - - - +
375A THR* 3.9 0.3 - - - +
376A ALA* 3.5 5.4 - - + +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLN 2.8 13.4 + - - +
38A ILE 3.6 3.8 - - - +
40A ASP* 1.3 77.6 - - - +
42A VAL* 1.3 58.5 + - - +
44A ASP* 3.3 4.9 + - - +
45A ALA* 2.9 29.1 + - - +
83A VAL* 4.2 11.3 - - + +
87A THR* 3.2 27.8 - - - +
373A GLN* 3.4 22.6 - - - +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.0 22.6 + - + +
39A SER 3.8 5.6 - - - +
41A ALA* 1.3 78.5 - - - +
43A LEU* 1.3 60.1 + - - +
45A ALA* 3.6 2.4 + - + +
46A HIS* 3.2 24.0 + - + -
55A VAL* 5.1 0.9 - - + -
57A CYS* 4.2 13.9 - - - -
68A LEU* 4.1 27.6 - - + -
72A ILE* 4.1 15.7 - - + -
80A TYR* 3.6 28.0 - - + -
83A VAL* 3.4 24.9 - - + -
84A VAL* 4.9 1.1 - - + -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER 3.2 14.5 + - - +
40A ASP* 3.6 10.8 - - - +
41A ALA 3.2 0.4 - - - -
42A VAL* 1.3 74.4 - - - +
44A ASP* 1.3 64.2 + - - +
46A HIS* 3.2 3.1 + - - +
47A LEU* 3.1 34.8 + - + +
55A VAL* 3.6 38.3 - - + +
285A GLY* 5.4 0.2 - - - -
286A LYS 3.4 28.3 - - - +
287A ASP* 3.8 15.3 - - + -
293A ARG* 3.7 11.2 - - - +
372A TYR* 3.4 34.1 - - + -
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Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASP 2.9 16.3 + - - +
41A ALA* 3.3 6.7 + - - +
43A LEU* 1.3 74.5 - - - +
45A ALA* 1.3 63.4 + - - +
46A HIS 2.9 2.4 + - - -
47A LEU* 3.0 11.4 + - - +
48A LYS* 3.1 25.1 + - - +
370A PRO* 3.3 35.3 - - + +
371A ILE 4.3 0.5 - - - -
372A TYR* 3.1 27.5 + - - +
373A GLN* 3.1 29.5 + - - +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA 2.9 17.5 + - - +
42A VAL* 3.7 7.4 - - - +
43A LEU 3.4 0.4 - - - -
44A ASP* 1.3 74.8 - - - +
46A HIS* 1.3 58.8 + - - +
48A LYS* 4.4 15.8 + - - +
49A GLN* 4.3 10.4 + - - +
78A ILE* 3.5 27.4 - - + +
83A VAL* 4.0 25.4 - - + -
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Residues in contact with HIS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.2 24.8 + - + +
43A LEU 3.2 7.3 + - - +
44A ASP 2.9 1.0 + - - -
45A ALA* 1.3 76.5 - - - +
47A LEU* 1.3 62.6 + - - +
48A LYS 3.2 0.4 - - - -
49A GLN* 3.0 5.2 + - - +
50A ASP* 2.8 31.1 + - - +
53A ALA* 3.7 13.7 - - + +
55A VAL* 4.1 10.3 - - + -
72A ILE* 3.3 20.1 - - + +
74A SER* 2.8 33.8 + - - -
76A ALA* 4.4 0.6 - - - +
78A ILE* 3.7 25.9 - - + +
80A TYR* 3.0 30.4 + - - -
113A GLN* 3.7 15.3 - - - -
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.1 37.6 + - + +
44A ASP 3.0 4.8 + - - +
46A HIS* 1.3 77.6 - - - +
48A LYS* 1.3 61.5 + - - +
49A GLN 3.1 1.2 + - - -
50A ASP 3.3 21.3 + - - +
51A PRO* 3.3 21.7 - - - +
53A ALA* 4.4 10.3 - - + +
288A TYR* 4.1 22.4 - - + -
368A LYS* 3.3 28.5 - - - +
369A LYS 4.1 4.0 - - - +
370A PRO* 4.3 12.0 - - + +
372A TYR* 3.6 34.8 - - + -
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 3.1 23.8 + - - +
45A ALA* 4.4 9.9 - - - +
47A LEU* 1.3 77.0 - - - +
49A GLN* 1.3 63.7 + - + +
51A PRO* 5.4 0.4 - - - -
370A PRO* 3.8 31.8 - - + +
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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