Contacts of the helix formed by residues 42 - 57 (chain C) in PDB entry 1HQ3
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 ARG 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C TYR* 1.3 82.8 - - + +
43C PRO* 1.3 80.9 - - + +
44C GLY* 3.0 34.7 - - - +
45C THR* 3.0 23.1 + - - +
46C VAL* 3.0 11.6 + - - +
44D LYS* 3.5 18.8 - - - +
45D ARG* 6.0 4.4 - - - +
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Residues in contact with PRO 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TYR 4.3 2.0 - - - +
42C ARG* 1.3 95.7 - - + +
44C GLY* 1.3 55.9 + - - +
46C VAL* 3.2 9.4 + - + +
47C ALA* 2.8 31.7 + - - +
45D ARG* 6.2 2.2 - - - +
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Residues in contact with GLY 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ARG* 3.0 35.6 - - - +
43C PRO* 1.3 79.9 - - - +
45C THR* 1.3 56.1 + - - +
47C ALA* 3.5 3.6 - - - +
48C LEU* 2.9 35.3 + - - +
44D LYS* 3.7 14.5 + - - -
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Residues in contact with THR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TYR* 3.7 31.9 - - + +
42C ARG* 3.0 25.3 + - - +
44C GLY* 1.3 75.2 - - - +
46C VAL* 1.3 61.4 + - - +
48C LEU* 3.7 9.3 + - - +
49C ARG* 3.2 31.6 + - - +
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Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 4.0 20.9 - - + +
42C ARG 3.0 15.3 + - - +
43C PRO* 3.6 9.4 - - + +
45C THR* 1.3 74.3 - - - +
47C ALA* 1.3 67.5 + - - +
49C ARG* 3.2 27.0 + - - +
50C GLU* 3.0 40.4 + - + +
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C PRO 2.8 17.7 + - - +
44C GLY* 3.5 5.6 - - - +
46C VAL* 1.3 76.6 - - - +
48C LEU* 1.3 59.3 + - - +
50C GLU* 2.8 21.6 + - - +
51C ILE* 2.9 17.1 + - - +
39D ARG* 3.9 21.3 - - - +
44D LYS* 3.2 37.2 - - + +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLY 2.9 13.8 + - - +
45C THR* 4.0 8.1 - - - +
47C ALA* 1.3 75.3 - - - +
49C ARG* 1.3 61.4 + - - +
51C ILE* 3.4 15.8 + - + +
52C ARG* 3.2 41.1 + - - +
44D LYS* 3.2 35.0 - - + +
111E ILE* 4.1 28.2 - - + +
115E LEU* 3.8 9.2 - - + +
116E LEU* 4.2 9.9 - - + -
117E PRO* 3.7 31.6 - - + -
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TYR* 4.0 30.3 - - - +
45C THR* 3.2 28.8 + - - +
46C VAL* 3.2 32.3 + - - +
47C ALA 3.1 0.4 - - - -
48C LEU* 1.3 76.9 - - - +
50C GLU* 1.3 59.6 + - + +
52C ARG* 3.4 9.4 + - - +
53C ARG* 3.0 28.0 + - + +
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C VAL* 3.0 31.7 + - + +
47C ALA 2.8 8.7 + - - +
49C ARG* 1.3 75.4 - - + +
51C ILE* 1.3 55.3 + - - +
53C ARG* 3.1 8.7 + - - +
54C TYR* 2.7 48.1 + - + -
505C PO4 2.9 36.3 + - - +
35D ARG* 4.4 11.5 + - - +
39D ARG* 2.7 48.8 + - + +
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Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ALA 2.9 14.7 + - - +
48C LEU* 3.7 26.5 - - + +
50C GLU* 1.3 74.3 - - - +
52C ARG* 1.3 65.2 + - - +
55C GLN* 2.8 48.5 + - - +
39D ARG* 3.5 27.5 - - - +
42D GLY* 3.6 18.4 - - - +
43D VAL 3.6 28.0 - - - +
44D LYS* 4.0 9.9 - - + +
111E ILE* 3.9 21.1 - - + -
115E LEU* 5.0 0.2 - - + -
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 3.2 30.4 + - - +
49C ARG* 3.8 9.7 - - - +
51C ILE* 1.3 81.1 - - - +
53C ARG* 1.3 61.7 + - - +
55C GLN* 5.3 0.2 - - - -
56C LYS* 2.7 50.4 + - - +
111E ILE* 3.6 23.9 - - + +
116E LEU* 3.8 24.9 - - - +
117E PRO* 5.4 2.4 - - - +
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Residues in contact with ARG 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ARG* 3.0 16.3 + - + +
50C GLU* 3.1 9.8 + - - +
52C ARG* 1.3 77.8 - - - +
54C TYR* 1.3 95.3 + - + +
56C LYS* 3.3 12.9 + - - +
57C SER* 3.3 14.1 + - - -
59C GLU* 5.4 4.2 + - - -
505C PO4 2.4 32.6 + - - -
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Residues in contact with TYR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLU* 2.7 40.3 + - + +
51C ILE 4.3 0.2 - - - +
53C ARG* 1.3 107.2 + - + +
55C GLN* 1.3 60.0 + - - +
56C LYS 3.3 0.5 + - - -
57C SER* 3.3 13.3 + - - +
59C GLU* 4.3 16.2 - - - -
61C LEU* 4.1 19.5 - - + -
505C PO4 3.0 33.0 + - - -
36D ARG* 3.2 40.6 + - + +
39D ARG* 3.9 15.3 - - + -
40D ARG* 3.0 47.6 + - + +
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Residues in contact with GLN 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ILE* 2.8 38.4 + - + +
54C TYR* 1.3 72.4 - - - +
56C LYS* 1.3 67.0 + - - +
57C SER 3.4 2.0 - - - +
39D ARG 3.9 2.0 - - - +
40D ARG* 3.2 26.3 + - - +
41D GLY 4.2 1.0 - - - -
42D GLY* 3.6 17.2 - - - +
81E ARG* 3.2 19.2 + - - -
107E VAL* 3.4 20.9 + - + +
108E LEU 4.1 5.8 + - - -
109E PRO* 3.5 12.4 - - + +
110E ASN 2.7 47.8 + - - +
111E ILE* 4.1 2.8 - - - +
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ARG* 2.7 53.3 + - - +
53C ARG* 3.3 5.6 + - - +
54C TYR 3.1 0.6 - - - -
55C GLN* 1.3 86.7 + - - +
57C SER* 1.3 61.3 + - - +
58C THR* 4.1 1.9 + - - +
81E ARG* 3.9 18.7 + - - +
109E PRO* 3.5 38.7 - - + +
111E ILE* 6.1 0.4 - - - +
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C ARG* 3.3 15.8 + - - -
54C TYR* 3.3 16.8 + - - +
55C GLN 4.3 2.3 - - - +
56C LYS* 1.3 83.1 - - - +
58C THR* 1.3 61.4 + - - +
59C GLU* 2.8 40.6 + - - +
40D ARG* 2.9 21.0 + - - -
81E ARG* 4.7 0.2 + - - -
106E GLY* 4.2 5.7 - - - -
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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