Contacts of the helix formed by residues 43 - 56 (chain T) in PDB entry 6QX2
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 LYS 43 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T ARG 3.4 24.9 - - - +
34T ALA* 3.4 24.1 + - - +
35T LEU 4.1 3.1 - - - -
36T PRO* 4.1 18.2 - - + -
41T GLY 4.2 0.8 + - - +
42T LEU* 1.3 73.7 - - - +
44T PRO* 1.4 73.6 - - + +
45T VAL* 4.4 4.7 - - + +
46T HIS* 3.1 29.2 + - + +
47T ARG* 3.1 19.6 + - - +
172T ALA* 5.2 5.2 - - - +
173T SER 2.7 33.0 + - - +
174T GLY* 3.8 4.0 - - - -
5W G 3.6 3.6 + - - -
6W T 3.2 36.0 + - - +
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Residues in contact with PRO 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31T VAL 5.0 2.5 - - - +
32T ALA* 3.6 35.4 - - + +
33T ARG* 3.8 12.6 - - - +
35T LEU 4.4 7.6 - - - +
42T LEU 4.5 1.1 - - - +
43T LYS* 1.4 85.1 - - + -
45T VAL* 1.3 64.1 + - - +
47T ARG* 3.2 21.5 + - - +
48T ARG* 2.9 54.8 + - - +
79T HIS* 4.6 3.4 - - + -
338T LEU* 6.0 1.6 - - + -
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Residues in contact with VAL 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T ARG 5.3 0.2 + - - -
43T LYS* 3.3 4.9 - - + +
44T PRO* 1.3 77.6 - - - +
46T HIS* 1.3 74.1 + - + +
48T ARG* 3.6 2.1 + - - +
49T ILE* 3.1 44.9 + - + +
74T VAL* 5.2 0.4 - - + +
79T HIS* 3.4 41.2 - - + +
85T SER 4.4 0.4 - - - +
86T ILE* 4.1 11.4 - - + -
89T ALA* 4.0 21.1 - - + -
6W T 4.0 25.8 - - - +
7W A 3.8 9.1 + - - +
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Residues in contact with HIS 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41T GLY 5.7 0.4 + - - -
42T LEU* 4.0 20.7 - - + +
43T LYS* 3.1 40.1 + - + +
45T VAL* 1.3 75.7 - - + +
47T ARG* 1.3 65.4 + - - +
49T ILE* 3.2 4.2 + - - +
50T LEU* 3.0 29.2 + - - +
89T ALA* 3.9 21.7 + - + +
92T ARG* 5.6 1.0 + - - +
93T MET* 3.9 28.9 - - + +
99T TYR* 3.9 18.5 + - - -
6W T 3.2 42.5 + - - -
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Residues in contact with ARG 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T ASP* 3.6 13.5 - - - +
40T ASP* 2.9 32.0 + - - -
42T LEU* 3.0 36.1 + - + +
43T LYS 3.1 6.3 + - - +
44T PRO* 3.5 29.0 - - - +
46T HIS* 1.3 76.4 - - - +
48T ARG* 1.3 59.0 + - + +
50T LEU* 3.3 3.6 + - - +
51T TYR* 2.9 31.1 + - - +
157T PRO* 3.3 30.5 - - + +
158T SER 3.6 13.4 + - - -
159T VAL* 3.4 14.3 - - - +
160T LEU* 3.8 20.9 - - + +
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Residues in contact with ARG 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32T ALA* 5.7 4.8 + - - +
44T PRO* 2.9 33.2 + - + +
45T VAL 3.9 4.0 - - - +
47T ARG* 1.3 74.9 - - + +
49T ILE* 1.3 60.6 + - - +
51T TYR* 3.9 5.3 - - - +
52T GLY* 2.9 26.3 + - - -
74T VAL* 3.9 14.9 - - + +
78T TYR* 3.3 43.9 + - + -
79T HIS* 3.0 37.9 + - + +
80T PRO* 4.5 5.8 - - - +
81T HIS* 4.9 3.8 + - - -
147T ILE* 6.0 1.2 - - - +
150T TYR* 6.1 1.4 - - - +
156T GLU* 2.8 39.4 + - + +
157T PRO* 6.4 0.9 - - + -
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Residues in contact with ILE 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45T VAL* 3.1 29.2 + - + +
46T HIS 3.2 6.0 + - - +
48T ARG* 1.3 74.6 - - - +
50T LEU* 1.3 57.9 + - - +
52T GLY* 3.2 2.9 + - - -
53T LEU* 2.9 41.0 + - + +
70T ILE* 5.0 5.1 - - + +
74T VAL* 3.9 13.9 - - + +
86T ILE* 3.5 40.6 - - + +
89T ALA* 4.1 2.7 - - + -
90T MET* 3.9 27.8 - - + +
93T MET* 3.6 28.7 - - + -
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Residues in contact with LEU 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T LEU* 4.1 16.6 - - + -
46T HIS 3.0 17.6 + - - +
47T ARG 3.9 3.4 - - - +
49T ILE* 1.3 74.8 - - - +
51T TYR* 1.3 60.2 + - - +
53T LEU* 3.4 19.5 + - + +
54T ASN* 3.2 21.3 + - - +
93T MET* 4.1 19.5 - - + -
103T LEU* 3.9 32.8 - - + +
104T VAL* 4.2 3.1 - - + -
128T MET* 5.2 0.2 - - - +
132T THR* 4.0 16.6 - - + -
135T LEU* 3.6 31.2 - - + -
136T LEU* 3.7 9.3 - - + +
160T LEU* 4.4 11.0 - - + -
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Residues in contact with TYR 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47T ARG 2.9 18.6 + - - +
48T ARG* 4.0 4.3 - - + +
50T LEU* 1.3 73.0 - - - +
52T GLY* 1.3 60.4 + - - +
54T ASN* 3.2 9.3 + - - +
55T GLU* 2.9 68.0 + - + +
78T TYR* 3.6 27.8 - + - -
136T LEU* 4.5 4.0 - - - +
139T ILE* 3.7 22.4 - - + -
140T ASN* 6.0 0.9 - - - -
146T PHE* 3.6 18.2 - + - -
155T ARG* 3.6 19.0 + - - +
156T GLU* 4.7 0.4 - - + -
157T PRO* 3.4 42.0 - - + -
160T LEU* 5.0 2.7 - - + +
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Residues in contact with GLY 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48T ARG 2.9 17.1 + - - -
49T ILE 3.2 4.9 + - - -
51T TYR* 1.3 74.2 - - - +
53T LEU* 1.3 63.8 + - - +
55T GLU* 3.5 3.3 + - - +
56T GLN* 3.2 29.8 + - - +
58T MET* 4.0 2.6 - - - +
70T ILE* 5.7 0.7 - - - -
73T ASP* 4.1 9.6 - - - -
74T VAL* 4.4 6.1 - - - -
78T TYR* 4.0 18.2 - - - -
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Residues in contact with LEU 53 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49T ILE* 2.9 27.8 + - + +
50T LEU* 3.5 29.8 - - + +
51T TYR 3.3 0.2 - - - -
52T GLY* 1.3 75.8 - - - +
54T ASN* 1.3 57.8 - - - +
56T GLN 3.5 1.4 + - - -
57T GLY 3.3 3.1 + - - -
58T MET* 2.8 48.9 + - + +
70T ILE* 3.7 39.0 - - + +
90T MET* 5.5 1.6 - - + -
104T VAL* 4.4 10.3 - - + -
126T ALA* 5.5 1.1 - - + -
127T ARG* 4.3 12.1 - - - +
128T MET* 3.7 30.5 - - + +
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Residues in contact with ASN 54 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50T LEU 3.2 10.7 + - - +
51T TYR* 3.2 12.2 + - - +
52T GLY 3.2 0.4 - - - -
53T LEU* 1.3 77.5 - - - +
55T GLU* 1.3 71.5 + - - +
57T GLY* 3.1 17.8 + - - -
59T THR* 5.1 3.8 - - - +
128T MET* 3.2 22.0 - - + +
133T LEU* 5.5 1.9 - - - +
136T LEU* 3.7 22.6 - - + +
139T ILE* 3.8 25.7 - - - +
140T ASN* 5.1 4.8 - - - +
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Residues in contact with GLU 55 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51T TYR* 2.9 64.0 + - + +
52T GLY* 4.0 3.6 - - - +
53T LEU 3.4 0.2 - - - -
54T ASN* 1.3 87.5 + - - +
56T GLN* 1.3 74.2 + - - +
57T GLY 3.3 1.7 + - - -
78T TYR* 3.6 12.6 - - - +
139T ILE* 5.7 0.5 - - - +
140T ASN* 5.2 7.4 + - - +
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Residues in contact with GLN 56 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52T GLY 3.2 12.9 + - - +
54T ASN 3.3 0.2 - - - -
55T GLU* 1.3 91.4 + - - +
57T GLY* 1.3 64.4 + - - +
58T MET* 2.9 36.9 + - + +
73T ASP* 3.5 22.5 + - + +
77T LYS* 3.4 23.8 + - - +
78T TYR* 5.2 0.2 + - - -
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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