Contacts of the helix formed by residues 64 - 78 (chain X) in PDB entry 2QW0
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 SER 64 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X PRO* 3.6 5.1 + - - -
63X ASN* 1.3 77.3 - - - +
65X ALA* 1.3 65.3 + - - +
66X ASP* 3.1 12.4 + - - +
67X VAL* 3.0 29.5 + - - +
68X VAL* 3.2 22.4 + - - +
129X LEU* 4.2 4.9 - - - +
205X LEU* 4.4 1.8 - - - +
225X TYR* 6.3 0.2 - - - -
227X VAL* 3.7 15.9 - - - +
229X GLU* 4.4 12.6 - - - -
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Residues in contact with ALA 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21X LEU* 4.3 17.5 - - + +
23X VAL* 3.7 27.3 - - + +
28X LEU* 4.2 15.7 - - + -
30X LEU* 5.5 1.3 - - + -
64X SER* 1.3 75.6 - - - +
66X ASP* 1.3 68.4 + - - +
68X VAL* 3.3 6.3 + - - +
69X ILE* 3.1 29.9 + - + +
136X GLY* 5.2 1.1 - - - +
227X VAL* 3.9 12.5 - - + +
229X GLU* 5.3 1.6 + - - -
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Residues in contact with ASP 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64X SER* 3.0 9.9 + - - +
65X ALA* 1.3 81.1 - - - +
67X VAL* 1.3 57.4 + - - +
69X ILE* 3.3 2.9 + - - +
70X ALA* 3.0 23.6 + - - +
129X LEU* 3.8 12.7 - - + +
133X VAL* 3.4 39.7 - - + +
134X ARG* 3.8 5.0 + - - -
135X ASP* 2.9 26.6 + - - +
136X GLY* 2.7 28.5 + - - -
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Residues in contact with VAL 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X VAL* 3.7 29.6 - - + -
61X ALA* 3.7 21.8 - - + +
62X PRO 3.9 7.4 - - - +
64X SER* 3.0 35.8 + - - +
66X ASP* 1.3 74.1 - - - +
68X VAL* 1.3 64.8 + - - +
70X ALA* 4.3 0.9 - - + -
71X ILE* 2.9 37.0 + - + +
106X VAL* 6.1 0.2 - - + -
129X LEU* 3.8 17.4 - - + +
205X LEU* 3.7 20.0 - - + -
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Residues in contact with VAL 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21X LEU* 4.2 19.3 - - + -
35X LEU* 4.8 3.6 - - + -
64X SER 3.2 14.5 + - - +
65X ALA* 3.4 10.5 - - - +
67X VAL* 1.3 77.6 - - - +
69X ILE* 1.3 65.1 + - - +
71X ILE* 3.9 5.6 - - - +
72X LEU* 3.1 36.9 + - + +
205X LEU* 4.0 18.2 - - + -
215X LEU* 3.8 37.7 - - + -
225X TYR* 4.4 17.0 - - + -
227X VAL* 5.4 0.2 - - + -
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Residues in contact with ILE 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21X LEU* 4.7 1.3 - - + -
30X LEU* 4.3 9.9 - - + -
35X LEU* 3.8 20.2 - - + -
38X ARG* 4.1 34.8 - - + +
39X VAL* 4.2 7.8 - - - +
42X VAL* 3.9 26.7 - - + -
65X ALA 3.1 16.3 + - - +
66X ASP 3.6 6.7 - - - +
67X VAL 3.2 0.2 - - - -
68X VAL* 1.3 77.1 - - - +
70X ALA* 1.3 57.7 + - - +
72X LEU* 3.8 1.2 - - - +
73X ALA* 2.8 31.7 + - - +
133X VAL* 4.0 14.4 - - + -
136X GLY* 4.0 27.4 - - - +
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Residues in contact with ALA 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42X VAL* 4.7 4.9 - - - -
46X LEU* 5.1 0.5 - - - +
59X VAL* 5.7 1.3 - - + -
66X ASP 3.0 8.6 + - - +
67X VAL* 3.8 6.3 - - + +
69X ILE* 1.3 77.2 - - - +
71X ILE* 1.3 58.7 + - + +
73X ALA* 3.2 7.1 + - - +
74X LEU* 2.9 36.6 + - + +
106X VAL* 4.5 9.2 - - + -
129X LEU* 3.6 31.0 - - + -
132X LEU* 4.5 15.0 - - + -
133X VAL* 4.8 2.2 - - + +
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Residues in contact with ILE 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X VAL* 4.0 14.1 - - + -
67X VAL* 2.9 40.7 + - + +
68X VAL* 4.0 5.6 - - - +
70X ALA* 1.3 75.0 - - - +
72X LEU* 1.3 60.0 + - + +
74X LEU* 3.3 10.1 + - - +
75X HIS* 3.0 25.3 + - - +
81X PRO* 4.0 16.6 - - + +
83X LEU* 3.7 33.9 - - + -
157X PHE* 4.5 2.9 - - + -
205X LEU* 4.8 14.1 - - + -
211X PHE* 3.7 32.8 - - + -
215X LEU* 6.3 1.1 - - + -
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Residues in contact with LEU 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X VAL* 4.3 6.7 - - + -
5X ASN* 5.1 0.3 - - - +
8X LEU* 3.6 33.2 - - + -
35X LEU* 4.7 6.5 - - + -
36X ARG* 4.5 6.5 + - - +
39X VAL* 3.5 25.2 - - + +
68X VAL* 3.1 33.2 + - + +
71X ILE* 1.3 73.5 - - + +
73X ALA* 1.3 60.6 + - - +
75X HIS* 3.8 7.2 - - + +
76X ARG* 2.8 32.2 + - - +
211X PHE* 4.2 28.7 - - + -
215X LEU* 4.9 4.9 - - + -
216X VAL* 5.1 1.1 - - + -
219X LEU* 4.4 12.8 - - + -
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Residues in contact with ALA 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39X VAL* 3.8 20.3 - - - +
42X VAL* 3.6 35.7 - - + -
43X ALA* 3.8 8.4 - - - +
46X LEU* 4.5 2.7 - - + -
69X ILE 2.8 19.9 + - - +
70X ALA 3.3 5.2 - - - +
72X LEU* 1.3 77.3 - - - +
74X LEU* 1.3 57.6 + - - +
76X ARG* 3.3 2.6 + - - +
77X LEU* 2.8 30.5 + - - +
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Residues in contact with LEU 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X LEU* 3.8 16.8 - - + +
51X LEU* 3.7 28.0 - - + -
57X VAL* 3.8 31.2 - - + -
59X VAL* 3.6 31.0 - - + -
70X ALA* 2.9 20.1 + - + +
71X ILE* 3.5 8.7 - - - +
73X ALA* 1.3 76.3 - - - +
75X HIS* 1.3 62.9 + - - +
77X LEU* 3.3 6.0 + - - +
78X GLY 3.1 4.7 + - - -
79X ALA* 3.0 29.2 + - + -
81X PRO* 4.0 15.0 - - + -
106X VAL* 4.5 9.9 - - + -
132X LEU* 6.3 0.2 - - + -
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Residues in contact with HIS 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X THR* 4.6 0.6 - - - -
4X VAL* 3.6 18.8 + - + +
5X ASN* 3.0 47.3 + - + +
8X LEU* 6.0 0.4 - - + -
71X ILE 3.0 16.9 + - - +
72X LEU* 3.8 8.7 - - + +
73X ALA 3.3 0.2 - - - -
74X LEU* 1.3 75.8 - - - +
76X ARG* 1.3 60.6 + - - +
78X GLY* 3.1 10.6 + - - -
79X ALA 3.9 8.9 + - - -
81X PRO* 4.3 1.3 - - + +
150X ARG* 2.8 31.6 + - - -
156X ALA 4.6 5.5 + - - -
157X PHE* 3.4 33.9 - + + -
175X GLN* 3.6 30.6 + - - -
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Residues in contact with ARG 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X ASN* 3.6 24.0 - - - +
36X ARG* 4.5 0.9 - - - +
39X VAL* 3.6 21.3 - - + +
40X GLU* 3.1 36.6 + - - +
43X ALA* 4.0 12.3 - - + -
72X LEU 2.8 21.5 + - - +
73X ALA 3.6 3.6 - - - +
75X HIS* 1.3 71.1 - - - +
77X LEU* 1.3 64.4 + - - +
145X ILE* 2.9 40.6 + - - +
146X GLU 2.7 24.9 + - - -
147X ASP* 3.5 21.8 + - - +
148X PRO* 3.7 0.9 - - - +
150X ARG* 3.0 15.6 + - - +
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Residues in contact with LEU 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X ALA* 3.4 22.4 - - + +
46X LEU* 3.6 14.6 - - + -
47X HIS* 3.5 27.1 - - + +
51X LEU* 3.8 26.7 - - + +
52X ARG* 3.8 22.2 - - - +
53X PRO* 4.0 7.1 - - + +
73X ALA 2.8 14.2 + - - +
74X LEU* 3.5 10.3 - - - +
76X ARG* 1.3 76.5 + - - +
78X GLY* 1.3 59.2 + - - +
79X ALA* 3.9 7.9 - - + +
145X ILE* 4.1 22.4 - - + +
146X GLU 4.7 1.0 - - - +
148X PRO* 3.1 20.0 - - - +
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Residues in contact with GLY 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X PRO* 3.7 13.1 - - - +
54X GLN* 3.1 18.9 + - - +
74X LEU 3.1 3.0 + - - -
75X HIS* 3.1 11.3 + - - -
77X LEU* 1.3 78.2 - - - +
79X ALA* 1.3 67.0 + - - +
80X VAL* 4.3 3.6 - - - +
148X PRO* 3.8 14.8 - - - -
150X ARG* 4.4 2.9 - - - -
175X GLN* 5.8 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
------------------------------------------------------------
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