Contacts of the helix formed by residues 30 - 41 (chain D) 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 THR 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C ARG* 4.0 20.7 + - + +
27D GLN 5.2 1.3 + - - -
28D GLY 3.2 1.1 + - - -
29D ILE* 1.3 74.9 - - - +
31D LYS* 1.3 62.4 + - - +
32D PRO* 3.1 24.8 - - + +
33D ALA* 3.0 29.5 + - + +
34D ILE* 3.0 26.2 + - - +
36D ARG* 5.6 0.9 - - - +
55D ARG* 3.8 2.2 - - - +
612D CL 3.1 19.5 - - + +
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Residues in contact with LYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D THR* 1.3 71.6 + - - +
32D PRO* 1.3 68.8 - - + +
34D ILE* 3.2 2.6 + - - +
35D ARG* 2.8 45.0 + - - +
51D TYR* 3.5 51.5 - - + +
55D ARG* 3.6 14.8 - - - +
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Residues in contact with PRO 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D THR* 3.1 18.4 - - + +
31D LYS* 1.3 100.3 - - + +
33D ALA* 1.3 59.4 + - - +
35D ARG* 3.3 33.2 - - - +
36D ARG* 3.0 49.6 + - - +
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Residues in contact with ALA 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU* 3.5 24.1 - - - +
62C ILE* 4.1 12.6 - - + -
63C ARG* 5.8 0.4 - - + -
29D ILE* 5.0 1.8 - - + -
30D THR* 3.0 25.3 - - + +
32D PRO* 1.3 76.2 - - - +
34D ILE* 1.3 63.2 + - - +
36D ARG* 3.2 9.5 + - - +
37D LEU* 3.0 28.8 + - - +
612D CL 3.6 15.9 - - + -
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Residues in contact with ILE 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C LEU* 6.3 0.2 - - + -
104C PHE* 4.0 12.9 - - + -
29D ILE* 4.1 16.4 - - + +
30D THR 3.0 20.2 + - - +
31D LYS 3.7 4.3 - - - +
33D ALA* 1.3 75.4 - - - +
35D ARG* 1.3 64.7 + - - +
37D LEU* 3.2 13.6 + - + +
38D ALA* 3.0 21.7 + - + +
46D ILE* 6.1 0.2 - - + -
50D ILE* 4.1 5.8 - - + -
51D TYR* 3.6 44.2 - - + +
54D THR* 4.0 28.5 - - + -
55D ARG* 4.0 27.6 - - + +
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Residues in contact with ARG 35 (chain D).
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* 4.4 10.6 + - - +
505C PO4 4.6 11.5 + - - -
31D LYS* 2.8 41.9 + - - +
32D PRO* 3.3 34.0 + - - +
33D ALA 3.2 0.2 - - - -
34D ILE* 1.3 78.4 - - - +
36D ARG* 1.3 69.8 + - + +
38D ALA* 3.2 5.2 + - - +
39D ARG* 3.0 53.1 + - + +
46D ILE* 3.9 23.5 - - + +
51D TYR* 4.2 11.0 - - - +
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Residues in contact with ARG 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TYR* 3.2 40.7 + - + +
61C LEU* 3.7 27.2 + - + +
505C PO4 3.1 32.8 + - - +
30D THR* 5.6 1.0 - - - +
32D PRO* 3.0 45.3 + - - +
33D ALA* 3.5 9.6 - - - +
35D ARG* 1.3 82.4 - - + +
37D LEU* 1.3 67.3 + - - +
39D ARG* 3.2 8.3 + - - +
40D ARG* 2.9 23.4 + - - +
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Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LEU* 3.9 15.7 - - + -
62C ILE* 4.0 28.3 - - + -
97C GLU* 3.5 33.7 - - + +
100C LEU* 4.1 20.0 - - + -
101C VAL* 3.7 27.2 - - + +
104C PHE* 3.9 15.2 - - + -
29D ILE* 6.1 0.2 - - + -
33D ALA 3.0 22.2 + - - +
34D ILE* 3.6 13.0 - - + +
36D ARG* 1.3 75.0 - - - +
38D ALA* 1.3 63.8 + - - +
40D ARG* 3.1 6.6 + - - +
41D GLY* 2.9 18.7 + - - -
54D THR* 6.3 0.2 - - + -
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PHE* 3.4 33.6 - - + -
119C ILE* 4.9 0.2 - - + -
34D ILE 3.0 13.1 + - - +
35D ARG 3.5 7.6 - - - +
37D LEU* 1.3 77.6 - - - +
39D ARG* 1.3 54.4 + - - +
41D GLY 3.2 6.2 + - - -
43D VAL* 2.8 43.5 + - + +
46D ILE* 3.8 22.9 - - + -
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Residues in contact with ARG 39 (chain D).
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* 3.9 13.7 - - - +
50C GLU* 2.7 44.4 + - + +
51C ILE* 3.5 31.2 - - - +
54C TYR* 3.9 18.2 - - + -
35D ARG* 3.0 37.0 + - + +
36D ARG* 3.2 7.2 + - - +
38D ALA* 1.3 71.9 - - - +
40D ARG* 1.3 62.3 + - - +
41D GLY 3.0 1.8 - - - -
42D GLY* 2.8 19.6 + - - -
43D VAL 2.8 34.9 + - - -
44D LYS* 2.9 23.8 + - - +
45D ARG 4.0 0.8 - - - +
46D ILE* 4.1 9.3 - - - +
603D CL 3.3 26.0 - - - +
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Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TYR* 3.0 30.9 + - + +
55C GLN* 3.2 24.0 + - - +
57C SER* 2.9 38.3 + - - -
58C THR* 3.9 6.6 + - - -
59C GLU 2.6 30.5 + - - -
60C LEU* 4.3 1.0 - - - +
61C LEU* 3.4 27.2 - - + +
97C GLU* 4.0 9.9 + - - +
101C VAL* 4.0 19.4 - - + +
105C GLU* 5.1 0.3 - - - +
36D ARG 2.9 12.7 + - - +
37D LEU* 3.4 9.5 - - - +
39D ARG* 1.3 76.6 - - - +
41D GLY* 1.3 57.5 + - - +
42D GLY 3.1 3.9 + - - -
106E GLY* 5.0 4.4 - - - -
107E VAL* 3.6 30.9 - - + +
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Residues in contact with GLY 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLN* 4.2 2.0 - - - -
101C VAL* 4.1 11.4 - - - +
104C PHE* 4.4 4.0 - - - -
105C GLU* 3.7 40.5 + - - +
108C ASN* 4.6 2.8 - - - +
37D LEU 2.9 12.6 + - - -
38D ALA 3.3 8.5 - - - -
39D ARG 3.0 0.4 - - - -
40D ARG* 1.3 77.0 - - - +
42D GLY* 1.3 60.8 - - - +
43D VAL* 3.4 4.6 + - - +
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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