Contacts of the helix formed by residues 43 - 56 (chain l) 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 l).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33l ARG 3.4 25.1 - - - +
34l ALA* 3.4 23.6 + - - +
35l LEU 4.1 0.7 - - - -
36l PRO* 4.1 20.0 - - + -
41l GLY 4.2 1.0 + - - -
42l LEU* 1.3 73.1 - - - +
44l PRO* 1.3 71.6 - - - +
45l VAL* 4.5 4.9 - - + +
46l HIS* 3.1 38.2 + - + +
47l ARG* 3.1 12.3 + - - +
172l ALA* 5.3 5.6 - - - +
173l SER 2.7 31.9 + - - +
174l GLY* 3.8 4.4 - - - -
5o G 3.6 3.0 + - - -
6o T 3.0 35.2 + - - +
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Residues in contact with PRO 44 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31l VAL 5.0 2.5 - - - +
32l ALA* 3.6 36.3 - - + +
33l ARG 3.8 10.8 - - - +
35l LEU 4.5 7.2 - - - +
42l LEU 4.5 1.1 - - - +
43l LYS* 1.3 85.6 - - + -
45l VAL* 1.3 63.4 + - - +
47l ARG* 3.2 19.9 + - - +
48l ARG* 2.9 55.1 + - - +
79l HIS* 4.7 3.1 - - + -
338l LEU* 6.1 0.9 - - + -
7o A 5.0 2.5 - - - +
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Residues in contact with VAL 45 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33l ARG 5.4 0.2 - - - +
43l LYS* 4.5 4.7 - - + +
44l PRO* 1.3 79.1 - - - +
46l HIS* 1.3 72.4 + - + +
48l ARG* 3.6 2.4 + - - +
49l ILE* 3.2 39.5 + - + +
74l VAL* 5.2 0.2 - - - +
79l HIS* 3.4 40.5 - - + +
85l SER 4.3 0.2 - - - +
86l ILE* 4.1 11.9 - - + -
89l ALA* 4.0 22.2 - - + -
6o T 4.1 24.7 - - - +
7o A 3.7 7.8 + - - +
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Residues in contact with HIS 46 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41l GLY 5.7 0.4 + - - -
42l LEU* 4.0 20.5 - - + +
43l LYS* 3.1 44.8 + - + +
45l VAL* 1.3 77.0 - - + +
47l ARG* 1.3 65.0 + - - +
49l ILE* 3.2 4.3 + - - +
50l LEU* 3.0 29.6 + - - +
89l ALA* 3.9 30.0 + - + +
92l ARG* 5.5 1.4 + - - +
93l MET* 3.9 27.3 - - + +
99l TYR* 3.9 18.8 + - - -
6o T 3.5 30.0 + - - -
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Residues in contact with ARG 47 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37l ASP* 3.6 13.9 - - - +
40l ASP* 2.9 32.8 + - - -
42l LEU* 3.0 35.2 + - + +
43l LYS 3.1 4.3 + - - +
44l PRO* 3.5 29.6 - - - +
46l HIS* 1.3 79.3 - - - +
48l ARG* 1.3 58.2 + - + +
50l LEU* 3.3 3.2 + - - +
51l TYR* 2.9 31.4 + - - +
157l PRO* 3.3 29.2 - - + +
158l SER 3.6 13.3 + - - -
159l VAL* 3.4 16.6 - - - +
160l LEU* 3.8 19.9 - - + +
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Residues in contact with ARG 48 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32l ALA* 5.8 2.8 + - - +
44l PRO* 2.9 31.8 + - - +
45l VAL 3.9 4.3 - - - +
47l ARG* 1.3 74.4 - - + +
49l ILE* 1.3 60.8 + - - +
51l TYR* 3.9 5.1 - - - +
52l GLY* 2.9 26.3 + - - -
74l VAL* 3.9 13.8 - - + +
78l TYR* 3.3 42.4 + - + -
79l HIS* 3.0 39.1 + - + +
80l PRO* 4.5 6.2 - - - +
81l HIS* 4.9 3.8 + - - -
147l ILE* 6.1 0.8 - - - +
150l TYR* 6.3 0.8 - - - +
156l GLU* 2.7 39.8 + - + +
157l PRO* 6.4 0.7 - - + -
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Residues in contact with ILE 49 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45l VAL* 3.2 28.8 + - + +
46l HIS 3.2 6.0 + - - +
48l ARG* 1.3 73.8 - - - +
50l LEU* 1.3 57.9 + - - +
52l GLY* 3.2 2.9 + - - -
53l LEU* 2.9 41.3 + - + +
70l ILE* 5.0 5.1 - - + +
74l VAL* 3.9 14.8 - - + +
86l ILE* 3.5 40.6 - - + +
89l ALA* 4.1 2.5 - - + -
90l MET* 3.9 28.0 - - + +
93l MET* 3.7 28.5 - - + -
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Residues in contact with LEU 50 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42l LEU* 4.1 17.3 - - + -
46l HIS 3.0 18.1 + - - +
47l ARG 3.9 3.6 - - - +
49l ILE* 1.3 75.7 - - - +
51l TYR* 1.3 60.9 + - - +
53l LEU* 3.4 19.8 + - + +
54l ASN* 3.2 22.2 + - - +
93l MET* 4.1 18.2 - - + -
103l LEU* 3.9 33.4 - - + +
104l VAL* 4.2 3.1 - - + -
132l THR* 4.0 16.8 - - + -
135l LEU* 3.6 30.7 - - + -
136l LEU* 3.7 8.6 - - + +
160l LEU* 4.3 11.7 - - + -
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Residues in contact with TYR 51 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47l ARG 2.9 18.0 + - - +
48l ARG* 3.9 4.3 - - - +
50l LEU* 1.3 74.2 - - - +
52l GLY* 1.3 59.6 + - - +
54l ASN* 3.2 8.7 + - - +
55l GLU* 2.9 69.4 + - + +
78l TYR* 3.6 28.0 - + - -
136l LEU* 4.4 4.6 - - - +
139l ILE* 3.7 22.9 - - + -
140l ASN* 6.1 0.7 - - - -
146l PHE* 3.6 19.1 - + - -
155l ARG* 3.6 18.7 + - - +
156l GLU* 4.8 0.2 - - + -
157l PRO* 3.4 42.4 - - + -
160l LEU* 5.0 2.2 - - + -
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Residues in contact with GLY 52 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48l ARG 2.9 15.7 + - - -
49l ILE 3.2 4.0 + - - -
51l TYR* 1.3 74.2 - - - +
53l LEU* 1.3 63.7 + - - +
55l GLU* 3.5 3.1 + - - +
56l GLN* 3.3 29.8 + - - +
58l MET* 4.6 2.0 - - - -
70l ILE* 5.8 0.7 - - - -
73l ASP* 3.8 9.6 - - - +
74l VAL* 4.4 6.3 - - - -
78l TYR* 3.9 18.4 - - - -
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Residues in contact with LEU 53 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49l ILE* 2.9 28.3 + - + +
50l LEU* 3.5 29.2 - - + +
51l TYR 3.3 0.2 - - - -
52l GLY* 1.3 76.6 - - - +
54l ASN* 1.3 58.2 + - - +
56l GLN 3.5 1.0 + - - -
57l GLY 3.3 2.8 + - - -
58l MET* 2.8 49.6 + - + +
70l ILE* 3.7 39.0 - - + -
90l MET* 5.5 2.0 - - + -
104l VAL* 4.4 11.2 - - + -
126l ALA* 5.2 0.4 - - + -
127l ARG* 4.4 10.8 - - - +
128l MET* 3.7 31.6 - - + +
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Residues in contact with ASN 54 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50l LEU 3.2 10.2 + - - +
51l TYR* 3.2 11.1 + - - +
52l GLY 3.2 0.6 - - - -
53l LEU* 1.3 78.6 - - - +
55l GLU* 1.3 72.7 + - - +
57l GLY* 3.1 17.8 + - - -
59l THR* 5.1 3.6 - - - +
128l MET* 3.2 20.9 - - + +
133l LEU* 5.4 2.6 - - - +
136l LEU* 3.7 24.2 - - + +
139l ILE* 3.9 24.7 - - - +
140l ASN* 5.1 4.9 - - - +
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Residues in contact with GLU 55 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51l TYR* 2.9 64.7 + - + +
52l GLY 4.0 2.7 - - - +
53l LEU 3.4 0.2 - - - -
54l ASN* 1.3 85.5 + - - +
56l GLN* 1.3 74.6 + - - +
57l GLY 3.3 1.5 + - - -
78l TYR* 3.6 12.3 - - - +
139l ILE* 5.7 0.5 - - - +
140l ASN* 5.3 7.6 + - - +
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Residues in contact with GLN 56 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69j ARG* 5.0 5.0 + - - -
52l GLY 3.3 14.2 + - - +
54l ASN 3.3 0.2 - - - -
55l GLU* 1.3 92.4 + - - +
57l GLY* 1.3 65.0 + - - +
58l MET* 2.9 36.2 + - + +
65l LYS* 4.4 4.0 + - - -
69l ARG* 3.9 25.3 + - - +
73l ASP* 3.5 22.7 + - + +
77l LYS* 3.4 24.2 + - - +
78l TYR* 5.1 0.4 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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