Contacts of the helix formed by residues 49 - 62 (chain M) in PDB entry 1HNW
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 THR 49 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47M ASP 3.4 5.4 + - - -
48M LEU* 1.3 71.3 - - - +
50M GLU* 1.3 67.2 + - + +
51M ALA* 3.0 32.3 - - + +
52M GLU* 2.7 29.2 + - + -
53M VAL* 2.8 23.3 + - - +
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Residues in contact with GLU 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48M LEU 3.6 2.6 + - - -
49M THR* 1.3 73.8 - - + +
51M ALA* 1.3 54.0 + - - +
53M VAL* 3.6 17.5 + - - +
54M VAL* 2.7 47.3 + - + +
57M ARG* 4.6 6.8 + - - -
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Residues in contact with ALA 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M THR* 2.9 17.0 - - + +
50M GLU* 1.3 75.7 - - - +
52M GLU* 1.3 59.5 + - + +
54M VAL* 2.7 35.5 + - - +
55M ARG* 3.0 18.6 + - + +
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Residues in contact with GLU 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M GLY 4.8 0.7 - - - +
39M ILE* 3.3 40.8 - - + +
40M ASN 4.8 1.4 + - - -
43M THR* 5.3 4.6 + - - +
47M ASP 4.3 2.4 - - - +
48M LEU* 3.3 13.7 - - + +
49M THR* 2.7 47.2 + - + +
51M ALA* 1.3 76.7 - - + +
53M VAL* 1.3 57.8 + - - +
54M VAL 2.8 0.3 + - - -
55M ARG* 3.0 31.2 + - - +
56M LEU* 2.8 32.9 + - - +
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Residues in contact with VAL 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M ALA* 3.3 37.0 - - + +
4M ILE* 5.1 4.7 - - + +
45M VAL* 6.3 0.2 - - + -
48M LEU* 3.7 34.7 - - + +
49M THR 2.8 22.4 + - - +
50M GLU* 3.8 16.4 - - - +
52M GLU* 1.3 70.9 - - - +
54M VAL* 1.3 56.8 + - - +
56M LEU* 4.2 6.0 - - - +
57M ARG* 2.9 48.1 + - - +
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Residues in contact with VAL 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M GLU* 2.7 37.9 - - + +
51M ALA* 2.7 14.4 + - - +
53M VAL* 1.3 77.3 - - - +
55M ARG* 1.3 64.6 + - + +
57M ARG* 3.3 7.8 + - - +
58M GLU* 2.9 47.2 + - + +
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Residues in contact with ARG 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M THR* 3.3 41.8 + - + +
38M GLY* 3.6 9.5 + - - -
39M ILE* 3.6 6.1 - - - +
51M ALA* 3.0 13.4 + - + +
52M GLU* 3.2 39.5 + - - +
54M VAL* 1.3 81.7 - - + +
56M LEU* 1.3 57.7 + - - +
58M GLU* 3.8 4.4 - - - +
59M TYR* 2.9 31.9 + - - +
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Residues in contact with LEU 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M ILE* 4.2 13.5 - - + -
15M VAL* 3.8 29.4 - - + -
19M LEU* 4.0 16.2 - - + -
33M ALA* 4.6 10.1 - - + +
34M LEU* 3.9 11.4 - - + -
37M THR* 3.6 8.9 - - + +
39M ILE* 3.8 19.7 - - + -
48M LEU* 4.1 12.1 - - + -
52M GLU 2.8 19.1 + - - +
53M VAL* 4.2 3.6 - - - +
55M ARG* 1.3 70.8 - - - +
57M ARG* 1.3 67.1 + - - +
59M TYR* 3.1 1.4 + - + -
60M VAL* 3.0 59.4 + - + +
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Residues in contact with ARG 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M ALA* 4.3 5.5 - - - +
3M ARG* 3.6 22.6 + - - +
4M ILE* 4.0 24.6 - - + +
50M GLU* 4.6 8.3 + - - -
53M VAL* 2.9 42.6 + - - +
54M VAL* 3.6 8.5 - - - +
56M LEU* 1.3 80.3 - - - +
58M GLU* 1.3 71.4 + - - +
61M GLU* 2.7 57.8 + - - +
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Residues in contact with GLU 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M VAL* 2.9 36.9 + - + +
55M ARG* 3.9 4.9 - - - +
57M ARG* 1.3 88.8 - - - +
59M TYR* 1.3 63.7 + - - +
61M GLU* 4.8 5.1 - - - +
62M ASN* 3.1 34.7 + - - +
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Residues in contact with TYR 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M GLU* 2.9 14.9 + - - -
33M ALA* 3.5 45.5 - - + -
36M LYS* 2.5 46.6 + - + +
37M THR* 3.9 10.1 - - - +
55M ARG 2.9 18.1 + - - +
56M LEU* 3.8 2.0 - - + +
58M GLU* 1.3 73.4 - - - +
60M VAL* 1.3 76.5 + - + +
62M ASN 2.6 28.5 - - - +
63M THR* 2.8 34.4 + - + +
64M TRP* 3.7 8.7 + + - -
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Residues in contact with VAL 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M ILE* 4.1 20.6 - - + -
5M ALA* 5.1 0.4 - - + -
19M LEU* 4.4 8.3 - - + -
22M ILE* 4.6 0.9 - - + -
25M ILE* 3.7 26.2 - - + -
33M ALA* 4.2 16.6 - - + -
56M LEU* 3.0 41.7 + - + +
59M TYR* 1.3 79.0 - - + +
61M GLU* 1.3 65.1 + - + +
63M THR* 3.1 19.9 - - - +
64M TRP* 3.7 6.5 + - + -
66M LEU* 3.6 24.2 - - + +
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Residues in contact with GLU 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M ILE* 3.1 24.3 - - + +
5M ALA* 4.1 18.0 - - + -
6M GLY 4.9 0.7 + - - -
57M ARG* 2.7 46.5 + - - +
58M GLU* 4.4 6.3 - - - +
59M TYR 3.2 1.0 - - - -
60M VAL* 1.3 76.6 - - - +
62M ASN* 1.3 68.2 + - - +
64M TRP 3.4 18.5 - - - +
66M LEU* 4.4 6.8 - - - +
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Residues in contact with ASN 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M GLU* 3.1 22.4 + - - +
59M TYR* 2.6 21.2 + - - +
61M GLU* 1.3 80.8 + - - +
63M THR* 1.3 58.7 + - - +
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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