Contacts of the helix formed by residues 42 - 55 (chain A) in PDB entry 2H3W
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 PRO 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A VAL 4.3 1.8 - - - +
41A PRO* 1.3 88.7 - - + +
43A LEU* 1.3 66.9 + - - +
44A GLN* 4.7 1.6 - - + +
45A GLN* 3.3 38.0 + - + +
46A SER* 3.1 21.0 + - - -
84A GLN* 4.1 3.1 - - - +
519A HIS* 3.8 0.2 - - - -
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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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41A PRO 3.5 2.4 + - - -
42A PRO* 1.3 72.6 - - - +
44A GLN* 1.3 68.4 + - + +
45A GLN 3.3 0.2 + - - -
46A SER* 3.4 1.6 + - - -
47A LEU* 3.1 47.3 + - + +
73A PHE* 4.2 5.6 - - + -
74A GLN* 4.2 19.1 - - + +
80A GLY* 3.5 34.5 - - - +
81A GLU* 3.7 8.5 - - + +
84A GLN* 3.6 22.8 + - + +
519A HIS* 3.9 7.4 - - + -
520A LEU* 5.9 0.2 - - + -
523A LEU* 3.6 31.0 - - + -
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Residues in contact with GLN 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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42A PRO* 3.4 1.7 - - + +
43A LEU* 1.3 79.1 - - + +
45A GLN* 1.3 62.2 + - - +
47A LEU* 4.0 1.2 - - - +
48A ASP* 3.2 22.7 + - - +
74A GLN* 3.3 52.4 + - + +
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Residues in contact with GLN 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 PRO* 4.2 9.1 - - - +
42A PRO* 3.3 41.7 + - + +
43A LEU 3.2 0.8 - - - -
44A GLN* 1.3 78.6 - - - +
46A SER* 1.3 62.4 + - - +
48A ASP* 3.2 8.4 + - - +
49A TYR* 3.1 54.4 + - + +
514A GLU* 3.9 30.5 + - - +
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Residues in contact with SER 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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41A PRO* 3.5 15.9 - - - +
42A PRO 3.1 5.1 + - - -
43A LEU 4.0 1.6 - - - -
45A GLN* 1.3 80.2 + - - +
47A LEU* 1.3 58.1 + - - +
49A TYR* 3.3 5.7 + - - -
50A TYR* 2.9 29.1 + - - +
514A GLU 5.1 0.2 + - - -
515A ALA 3.8 2.8 + - - -
516A PHE* 3.5 29.2 - - - +
519A HIS* 2.8 34.4 + - - -
520A LEU* 4.6 7.6 - - - -
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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 29.9 + - + +
44A GLN 4.0 0.2 - - - +
46A SER* 1.3 74.0 - - - +
48A ASP* 1.3 65.6 + - - +
50A TYR* 3.3 8.8 + - + +
51A LEU* 3.0 30.7 + - - +
70A VAL* 3.8 20.4 - - + +
73A PHE* 4.0 15.5 - - + -
74A GLN* 3.1 44.6 - - + +
520A LEU* 4.2 20.6 - - + -
537A ILE* 4.1 25.6 - - + -
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Residues in contact with ASP 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 GLN 3.2 14.6 + - - +
45A GLN* 3.2 11.8 + - - +
47A LEU* 1.3 75.2 - - - +
49A TYR* 1.3 73.3 + - - +
51A LEU* 3.3 12.9 + - - +
52A LYS* 3.0 53.8 + - - +
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Residues in contact with TYR 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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45A GLN* 3.1 51.5 + - + +
46A SER* 3.7 5.8 - - - +
48A ASP* 1.3 87.2 - - - +
50A TYR* 1.3 62.6 + - - +
52A LYS* 3.3 17.6 + - + +
53A ALA* 3.0 24.9 + - - +
506A TYR* 5.8 3.8 - - + -
509A ARG* 3.2 46.9 + - - -
514A GLU* 3.9 20.6 + - - -
515A ALA* 5.7 0.2 - - - -
516A PHE* 3.6 20.9 - + + -
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Residues in contact with TYR 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 SER 2.9 16.9 + - - +
47A LEU* 3.4 12.6 - - + +
48A ASP 3.1 0.2 - - - -
49A TYR* 1.3 77.7 - - - +
51A LEU* 1.3 63.1 + - - +
53A ALA* 3.2 2.8 + - - +
54A LEU* 3.1 61.4 + - + +
66A THR* 4.0 12.5 - - + +
70A VAL* 4.6 10.8 - - + -
469A ARG* 5.7 0.7 - - - -
516A PHE* 3.4 34.9 - + + -
520A LEU* 3.8 13.2 - - + -
537A ILE* 4.6 20.3 + - + -
540A ASP* 5.1 0.3 + - - -
542A SER* 3.8 1.9 - - - -
543A TYR* 3.3 52.5 + + - +
546A ALA* 4.2 8.1 - - + -
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Residues in contact with LEU 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 LEU 3.0 21.0 + - - +
48A ASP* 3.3 11.4 + - - +
50A TYR* 1.3 76.1 - - + +
52A LYS* 1.3 61.5 + - + +
54A LEU* 3.4 4.6 + - + -
55A GLN* 3.3 8.1 + - - +
63A TRP* 2.8 48.4 + - + +
66A THR* 3.8 19.1 - - + -
67A LYS* 4.0 37.2 - - + +
70A VAL* 3.8 38.1 - - + -
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Residues in contact with LYS 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 ASP* 3.0 47.5 + - - +
49A TYR* 3.6 21.8 - - + +
50A TYR 3.2 0.2 - - - -
51A LEU* 1.3 77.7 - - + +
53A ALA* 1.3 60.1 + - - +
54A LEU 3.3 0.7 + - - -
55A GLN* 3.4 6.8 + - - +
56A PRO* 3.3 16.8 - - - +
63A TRP* 5.9 0.4 - - - -
472A SER* 5.2 0.4 - - - -
473A ILE* 3.8 27.9 + - + +
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Residues in contact with ALA 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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49A TYR 3.0 17.0 + - - +
50A TYR* 3.2 5.1 + - + +
52A LYS* 1.3 76.5 - - - +
54A LEU* 1.3 60.1 + - + +
56A PRO* 3.5 15.1 - - - +
57A ILE* 3.7 13.1 - - - +
469A ARG* 3.8 35.8 + - + -
471A ALA 3.9 11.2 - - - +
472A SER* 5.3 3.1 - - - +
506A TYR* 4.7 6.7 - - + +
516A PHE* 4.0 7.4 - - + -
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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 TYR* 3.1 51.5 + - + +
51A LEU* 3.7 11.2 - - + +
52A LYS 3.1 0.4 - - - -
53A ALA* 1.3 76.5 - - - +
55A GLN* 1.3 66.0 + - - +
56A PRO* 3.2 2.9 - - - -
57A ILE* 2.9 18.7 + - + +
58A VAL* 3.0 31.9 + - + +
63A TRP* 4.0 7.9 - - + -
66A THR* 3.7 19.3 - - + -
542A SER* 3.5 30.3 - - - +
546A ALA* 3.6 19.5 - - + -
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Residues in contact with GLN 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 LEU 3.3 9.3 + - - +
52A LYS* 3.4 8.7 + - - +
54A LEU* 1.3 77.5 - - - +
56A PRO* 1.3 66.5 - - + +
57A ILE 3.5 0.2 + - - -
58A VAL* 3.5 14.8 - - - +
63A TRP* 3.7 24.6 + - + +
473A ILE* 3.6 37.3 - - + +
476A LEU* 5.4 0.3 - - - +
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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
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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