Contacts of the helix formed by residues 42 - 57 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39G HIS* 3.1 51.3 + - + +
40G ARG 3.6 2.9 + - - +
41G TYR* 1.3 80.8 - - - +
43G PRO* 1.3 82.3 - - + +
44G GLY* 3.1 5.4 - - - +
45G THR* 3.2 13.5 + - - +
46G VAL* 3.2 11.6 + - - +
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Residues in contact with PRO 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ARG* 1.3 98.7 - - + +
44G GLY* 1.3 57.8 + - - +
46G VAL* 3.1 9.8 + - + +
47G ALA* 2.8 29.9 + - - +
45H ARG* 6.2 1.6 - - - +
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Residues in contact with GLY 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ARG* 3.1 4.5 - - - +
43G PRO* 1.3 83.4 - - - +
45G THR* 1.3 61.3 + - - +
47G ALA* 3.3 5.8 + - - +
48G LEU* 3.0 30.9 + - - +
44H LYS* 4.0 21.9 - - - -
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Residues in contact with THR 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G HIS* 3.0 33.7 + - - +
40G ARG* 5.9 0.7 - - - +
41G TYR* 3.3 35.4 + - + +
42G ARG* 3.2 6.8 + - - +
44G GLY* 1.3 76.3 - - - +
46G VAL* 1.3 57.9 + - + +
48G LEU* 3.6 10.1 + - - +
49G ARG* 3.1 62.6 + - + +
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Residues in contact with VAL 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G TYR* 4.7 11.0 - - + +
42G ARG 3.2 13.9 + - - +
43G PRO* 3.1 12.5 + - + +
45G THR* 1.3 76.8 - - + +
47G ALA* 1.3 67.4 + - - +
49G ARG* 3.1 15.0 + - + +
50G GLU* 2.9 43.0 + - + +
39H ARG* 6.1 0.4 - - - +
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G PRO 2.8 19.2 + - - +
44G GLY* 3.6 6.1 - - - +
46G VAL* 1.3 72.7 - - - +
48G LEU* 1.3 58.1 + - - +
50G GLU* 3.1 5.9 + - - +
51G ILE* 2.8 33.0 + - - +
39H ARG* 3.7 26.7 - - - +
44H LYS* 3.1 35.9 - - + +
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Residues in contact with LEU 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 4.4 10.7 - - + +
115A LEU* 3.8 24.7 - - + +
116A LEU* 4.3 13.0 - - + -
117A PRO* 4.1 21.5 - - + -
44G GLY 3.0 23.5 + - - +
45G THR* 3.8 8.7 - - - +
46G VAL 3.2 0.2 - - - -
47G ALA* 1.3 73.4 - - - +
49G ARG* 1.3 64.6 + - - +
51G ILE* 3.4 17.2 + - + +
52G ARG* 3.1 44.2 + - - +
44H LYS* 4.1 21.5 - - + +
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Residues in contact with ARG 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G ARG* 4.0 7.3 - - - +
41G TYR* 2.7 48.4 + - - -
45G THR* 3.1 32.7 + - - +
46G VAL* 3.1 15.3 + - - +
48G LEU* 1.3 75.9 - - + +
50G GLU* 1.3 53.0 + - + +
52G ARG* 3.2 11.0 + - - +
53G ARG* 2.8 34.8 + - - +
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Residues in contact with GLU 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G VAL* 2.9 34.3 + - + +
47G ALA 3.2 8.7 - - - +
49G ARG* 1.3 75.0 - - + +
51G ILE* 1.3 65.9 + - - +
53G ARG* 3.2 9.3 + - - +
54G TYR* 2.9 44.3 + - + -
35H ARG* 3.9 16.1 + - - +
39H ARG* 2.9 35.9 + - + +
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Residues in contact with ILE 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 3.7 26.2 - - + -
47G ALA 2.8 20.1 + - - +
48G LEU* 3.7 23.8 - - + +
50G GLU* 1.3 72.3 - - - +
52G ARG* 1.3 59.7 + - - +
54G TYR 3.8 0.5 - - - -
55G GLN* 2.8 53.4 + - - +
39H ARG* 3.7 22.4 - - - +
42H GLY* 3.6 19.5 - - - +
43H VAL 3.4 28.3 - - - +
44H LYS* 4.0 9.6 - - + -
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Residues in contact with ARG 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.5 23.8 - - + +
116A LEU* 3.9 23.6 - - - +
117A PRO* 5.6 1.6 - - - +
48G LEU* 3.1 33.5 + - - +
49G ARG* 3.6 11.3 - - - +
51G ILE* 1.3 77.3 - - - +
53G ARG* 1.3 63.8 + - - +
55G GLN* 4.0 4.1 - - - +
56G LYS* 3.2 25.3 + - - +
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Residues in contact with ARG 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ARG 2.8 20.4 + - - +
50G GLU* 3.2 10.6 + - - +
52G ARG* 1.3 75.8 - - - +
54G TYR* 1.3 104.1 + - + +
56G LYS* 3.3 15.1 + - - +
57G SER* 3.3 14.6 + - - +
59G GLU* 5.1 6.3 + - - -
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Residues in contact with TYR 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G GLU* 2.9 44.4 + - + +
53G ARG* 1.3 112.3 + - + +
55G GLN* 1.3 61.1 + - - +
56G LYS 3.0 6.0 + - - -
57G SER* 3.4 19.2 + - - +
59G GLU* 4.0 12.6 - - - -
61G LEU* 3.9 17.3 - - + -
35H ARG* 6.3 0.4 - - + -
36H ARG* 3.4 44.9 + - + +
39H ARG* 3.9 15.7 - - + -
40H ARG* 2.8 46.1 - - + +
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Residues in contact with GLN 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 3.1 21.3 + - - -
107A VAL* 3.4 14.6 + - + +
108A LEU 4.0 8.0 + - - +
109A PRO* 3.5 15.1 - - + +
110A ASN 2.8 47.2 + - - +
111A ILE* 4.1 2.6 - - - +
51G ILE* 2.8 39.3 + - + +
52G ARG* 4.0 4.9 - - - +
54G TYR* 1.3 72.8 - - - +
56G LYS* 1.3 60.2 + - - +
57G SER 4.2 1.4 - - - +
105G GLU* 5.7 0.6 + - - -
39H ARG 4.0 2.7 - - - +
40H ARG* 3.0 32.3 + - - +
41H GLY 4.2 1.0 - - - -
42H GLY* 3.6 15.4 - - - +
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Residues in contact with LYS 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 3.8 20.8 + - - +
109A PRO* 5.3 3.6 - - + -
52G ARG 3.2 18.3 + - - +
53G ARG* 3.4 8.1 - - - +
54G TYR 3.0 0.2 - - - -
55G GLN* 1.3 80.7 - - - +
57G SER* 1.3 61.3 + - - +
58G THR* 4.6 1.6 - - - +
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Residues in contact with SER 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 4.6 0.3 + - - -
106A GLY* 4.2 4.7 - - - -
53G ARG* 3.3 11.2 + - - +
54G TYR* 3.4 15.9 + - - +
55G GLN 4.2 2.3 - - - +
56G LYS* 1.3 82.4 - - - +
58G THR* 1.3 64.6 + - - +
59G GLU* 3.7 23.3 + - - -
40H ARG* 3.2 29.9 + - - -
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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