Contacts of the helix formed by residues 37 - 55 (chain A) in PDB entry 1QFM
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 GLU 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASP 3.8 1.8 + - - +
36A SER* 1.3 73.0 - - - +
38A GLN* 1.3 65.6 + - - +
40A LYS* 2.9 34.1 + - - +
41A ALA* 2.9 33.2 + - - +
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Residues in contact with GLN 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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30A TRP* 3.7 24.2 - - + -
36A SER* 3.3 19.9 - - - +
37A GLU* 1.3 85.7 + - + +
39A THR* 1.3 57.8 + - - +
41A ALA* 3.4 1.1 + - - -
42A PHE 3.0 9.2 + - - -
793A GOL 2.8 36.3 + - - +
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Residues in contact with THR 39 (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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30A TRP* 3.3 16.5 + - - -
31A LEU* 3.6 20.6 - - + +
33A ASP 2.8 28.9 + - - +
34A PRO* 4.2 12.3 - - + +
36A SER* 3.0 13.1 + - - -
38A GLN* 1.3 72.8 - - - +
40A LYS* 1.3 67.3 + - - +
42A PHE* 3.1 3.6 + - - +
43A VAL* 3.0 25.4 + - + +
650A LEU* 3.8 28.5 - - + -
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Residues in contact with LYS 40 (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 PRO 4.0 15.0 - - - +
35A ASP* 3.7 13.4 + - - +
36A SER 3.0 21.5 + - - +
37A GLU* 2.9 39.1 + - - +
39A THR* 1.3 76.0 - - - +
41A ALA* 1.3 61.4 + - - +
43A VAL* 3.4 7.3 + - - +
44A GLU* 3.0 37.2 + - - +
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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 GLU 2.9 18.4 + - - +
38A GLN* 4.6 0.2 - - - -
40A LYS* 1.3 72.9 - - - +
42A PHE* 1.3 61.2 + - - +
44A GLU* 3.4 10.9 + - - +
45A ALA* 2.9 30.7 + - - +
793A GOL 3.4 19.0 - - - +
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Residues in contact with PHE 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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9A VAL* 3.6 32.1 - - + -
31A LEU* 3.7 26.0 - - + -
38A GLN 3.0 7.8 + - - +
39A THR 3.3 7.4 - - - +
41A ALA* 1.3 77.0 - - - +
43A VAL* 1.3 68.0 + - + +
45A ALA* 3.3 2.4 + - - +
46A GLN* 3.0 56.6 + - + +
650A LEU* 3.5 49.4 - - + -
653A ILE* 3.7 10.1 - - + -
654A ALA* 4.0 5.4 - - + -
672A ILE* 5.3 0.2 - - + -
793A GOL 3.2 40.5 - - - -
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Residues in contact with VAL 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 THR* 3.0 19.5 + - + +
40A LYS* 3.7 9.2 - - - +
42A PHE* 1.3 78.2 - - + +
44A GLU* 1.3 65.0 + - + +
46A GLN* 3.2 5.5 + - - +
47A ASN* 2.9 32.8 + - - +
650A LEU* 4.0 33.7 - - + -
674A VAL* 3.8 33.6 - - + +
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Residues in contact with GLU 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 LYS* 3.0 30.1 + - - +
41A ALA* 3.7 8.6 + - - +
43A VAL* 1.3 79.0 - - + +
45A ALA* 1.3 56.9 + - - +
47A ASN* 3.3 6.0 + - - +
48A LYS* 2.9 37.8 + - + +
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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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7A PRO* 3.6 34.0 - - + +
41A ALA 2.9 17.4 + - - +
42A PHE 3.8 4.0 - - - +
44A GLU* 1.3 76.0 - - - +
46A GLN* 1.3 61.5 + - - +
48A LYS* 3.5 23.6 + - - +
49A ILE* 3.6 8.0 + - - +
793A GOL 3.9 8.3 - - - +
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Residues in contact with GLN 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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7A PRO* 3.8 16.7 - - + +
9A VAL* 4.5 2.0 - - - +
42A PHE* 3.0 56.5 + - + +
43A VAL* 3.6 4.9 - - - +
45A ALA* 1.3 74.8 - - - +
47A ASN* 1.3 67.4 + - - +
49A ILE* 3.2 14.8 + - - +
50A THR* 3.1 26.5 + - - -
653A ILE* 4.5 1.1 - - - +
654A ALA* 5.4 0.2 - - - +
657A GLN* 3.0 42.8 + - - -
671A LEU* 5.5 0.2 - - - -
672A ILE* 3.5 32.3 + - + +
674A VAL* 5.9 1.1 - - + -
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Residues in contact with ASN 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 VAL* 2.9 29.9 + - - +
44A GLU* 3.9 5.5 - - - +
46A GLN* 1.3 77.0 - - - +
48A LYS* 1.3 62.3 + - + +
50A THR* 4.5 4.3 - - - -
51A VAL* 3.0 36.3 + - + +
672A ILE 3.9 0.7 - - - +
673A HIS* 3.3 18.7 + - - -
674A VAL* 2.9 46.8 + - - +
676A THR* 6.2 0.8 - - - +
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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
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44A GLU* 2.9 30.0 + - + +
45A ALA* 3.5 14.1 - - - +
46A GLN 3.1 0.2 - - - -
47A ASN* 1.3 78.5 - - + +
49A ILE* 1.3 61.4 + - + +
52A PRO* 3.0 23.8 - - - +
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Residues in contact with ILE 49 (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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4A PHE* 3.8 38.2 - - + +
5A GLN 3.8 16.8 - - - +
6A TYR* 3.8 20.9 - - + -
7A PRO* 3.8 26.2 - - + -
45A ALA 3.6 10.0 + - - +
46A GLN* 3.2 19.7 - - - +
48A LYS* 1.3 81.5 - - + +
50A THR* 1.3 68.3 + - - +
51A VAL 3.5 0.2 - - - -
52A PRO* 3.6 2.9 - - - +
53A PHE* 3.5 20.3 + - - +
671A LEU* 4.0 11.9 - - + -
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Residues in contact with THR 50 (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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46A GLN* 3.1 12.9 + - - -
47A ASN* 3.4 3.8 + - - -
49A ILE* 1.3 76.8 - - - +
51A VAL* 1.3 67.0 + - - +
53A PHE* 3.1 4.5 + - - +
54A LEU* 3.0 44.1 + - + +
634A LEU* 4.2 10.8 - - + -
671A LEU* 3.4 28.5 - - + +
672A ILE 2.7 31.6 + - - +
673A HIS* 4.0 12.8 - - + +
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Residues in contact with VAL 51 (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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47A ASN* 3.0 19.6 + - + +
48A LYS* 5.6 0.2 - - - -
50A THR* 1.3 76.2 - - - +
52A PRO* 1.4 70.3 - - + +
54A LEU* 3.2 8.1 + - + -
55A GLU* 3.0 51.2 + - + +
673A HIS* 3.8 31.9 - - + +
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Residues in contact with PRO 52 (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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48A LYS* 3.0 29.2 - - - +
49A ILE* 3.6 7.6 - - - +
51A VAL* 1.4 93.0 - - + +
53A PHE* 1.3 54.8 + - - +
55A GLU* 4.5 4.9 - - + +
56A GLN* 2.9 36.5 + - - +
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Residues in contact with PHE 53 (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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1A MET* 3.4 43.7 - - + -
2A LEU* 4.9 0.4 - - + -
4A PHE* 3.6 25.6 - + + -
49A ILE 3.5 13.4 + - - +
50A THR 3.1 8.8 + - - +
52A PRO* 1.3 79.7 - - - +
54A LEU* 1.3 65.9 + - + +
56A GLN* 3.8 2.4 + - - +
57A CSX 4.9 0.3 + - - -
669A PRO* 3.8 9.0 - - + -
671A LEU* 3.7 20.2 - - + -
699A PHE* 3.8 29.6 - + - -
702A ARG* 2.8 67.6 + - + +
703A CYS* 4.2 4.3 - - - -
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Residues in contact with LEU 54 (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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50A THR* 3.0 39.5 + - + +
51A VAL* 3.2 7.8 + - + +
53A PHE* 1.3 81.2 - - + +
55A GLU* 1.3 60.3 + - + +
57A CSX 4.8 3.1 + - - +
59A ILE* 5.6 1.0 - - - +
60A ARG* 3.5 23.2 - - - +
634A LEU* 4.5 9.2 - - + -
673A HIS* 5.0 7.9 - - + +
695A ASP* 3.7 55.6 - - + +
698A ALA* 3.7 10.3 - - + +
699A PHE* 3.8 33.7 - - + +
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Residues in contact with GLU 55 (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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51A VAL* 3.0 38.7 + - + +
52A PRO* 3.7 3.9 - - + +
54A LEU* 1.3 82.2 - - + +
56A GLN* 1.3 63.7 + - - +
57A CSX 3.5 7.5 + - - +
60A ARG* 3.9 34.9 + - - +
691A GLU* 5.5 0.3 - - - +
695A ASP* 5.5 0.4 - - - +
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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