Contacts of the helix formed by residues 63 - 77 (chain M) in PDB entry 7CRQ
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 63 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A A 4.0 17.9 - - - +
112A C 3.6 17.7 + - - +
28B GLY 5.8 0.9 - - - +
33B ALA* 5.9 2.0 - - + +
36B ARG* 3.8 29.5 - - - +
60M LEU 5.0 9.1 + - - -
61M LEU* 5.5 0.4 - - - +
62M ILE* 1.3 83.6 + - + +
64M LYS* 1.3 60.7 + - - +
65M LEU 3.5 0.4 - - - -
66M PRO* 3.5 25.3 - - + +
67M PHE* 3.0 30.2 + - - +
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Residues in contact with LYS 64 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A C 3.6 20.0 + - - +
60M LEU* 3.5 35.4 - - - +
62M ILE 4.4 6.0 + - - +
63M ARG* 1.3 73.6 - - - +
65M LEU* 1.3 59.9 + - + +
67M PHE* 3.4 2.8 + - - +
68M GLN* 2.9 33.6 + - - +
90M NLE 4.1 21.8 - - + +
93M GLN* 4.7 13.7 - - - +
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Residues in contact with LEU 65 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A A 4.1 34.1 - - + +
112A C 4.0 17.7 + - + +
64M LYS* 1.3 76.7 - - + +
66M PRO* 1.3 73.8 - - + +
68M GLN* 3.2 22.5 + - - +
69M ARG* 3.1 41.7 + - + +
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Residues in contact with PRO 66 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A A 4.0 26.9 - - - +
25B ASN* 4.7 6.8 - - - +
28B GLY* 3.8 31.0 - - - +
29B ILE* 5.0 5.2 - - + +
62M ILE* 5.9 0.9 - - + -
63M ARG* 3.5 31.4 - - + +
65M LEU* 1.3 95.9 - - + +
67M PHE* 1.3 60.2 + - - +
69M ARG* 3.6 21.4 + - - +
70M LEU* 3.6 12.0 + - - +
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Residues in contact with PHE 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 4.9 12.3 - - + -
58B LEU* 5.5 5.8 - - + -
62B LEU* 4.7 14.4 - - + -
62M ILE* 4.4 25.0 - - + +
63M ARG 3.0 20.5 + - - +
64M LYS 3.9 3.1 - - - +
66M PRO* 1.3 76.4 - - - +
68M GLN* 1.3 64.7 + - - +
70M LEU* 3.4 19.9 + - + +
71M VAL* 3.6 33.3 + - + +
89M VAL* 4.4 11.9 - - + -
92M LEU* 4.3 5.4 - - + -
93M GLN* 3.9 53.2 - - + +
96M SER* 4.1 22.4 - - - -
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Residues in contact with GLN 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M LYS* 2.9 20.7 + - - +
65M LEU* 3.2 22.1 + - - +
67M PHE* 1.3 79.3 - - + +
69M ARG* 1.3 66.7 + - + +
71M VAL* 3.7 4.0 + - - +
72M ARG* 3.6 50.8 + - - +
89M VAL* 4.3 27.3 - - + +
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Residues in contact with ARG 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A A 3.5 33.3 + - - -
22B LEU* 4.1 16.8 - - + +
25B ASN* 3.9 26.9 + - + +
28B GLY* 6.2 0.8 - - - -
65M LEU* 3.1 33.4 + - + +
66M PRO* 4.1 19.9 - - - +
67M PHE 3.3 0.4 - - - -
68M GLN* 1.3 80.3 - - + +
70M LEU* 1.3 57.0 + - - +
72M ARG* 3.4 7.5 + - - +
73M GLU* 3.0 28.1 + - - +
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Residues in contact with LEU 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN* 4.2 14.7 - - + +
26B ILE* 3.9 47.3 - - + +
29B ILE* 4.4 19.7 - - + -
58B LEU* 4.8 7.2 - - + -
59B LYS* 4.6 7.2 - - + +
62B LEU* 4.4 17.5 - - + -
66M PRO 3.6 8.3 + - - +
67M PHE* 3.4 16.7 + - + +
68M GLN 3.3 0.6 - - - -
69M ARG* 1.3 76.5 - - - +
71M VAL* 1.3 65.9 + - + +
73M GLU* 3.3 7.9 + - - +
74M ILE* 3.0 43.4 + - + +
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Residues in contact with VAL 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 4.9 12.6 - - + -
66B ILE* 4.5 9.9 - - + +
67M PHE* 3.6 36.2 + - + +
68M GLN* 4.1 8.3 - - - +
69M ARG 3.4 0.4 - - - -
70M LEU* 1.3 76.6 - - + +
72M ARG* 1.3 61.3 + - + +
74M ILE* 3.3 6.4 + - - +
75M ALA* 3.0 28.6 + - - +
84M PHE* 4.0 30.7 - - + -
89M VAL* 5.2 10.8 - - + -
92M LEU* 4.3 22.2 - - + -
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Residues in contact with ARG 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 4.3 16.3 - - + +
68M GLN* 3.6 41.9 + - - +
69M ARG* 3.4 10.4 + - - +
70M LEU 3.3 0.4 - - - -
71M VAL* 1.3 78.8 - - + +
73M GLU* 1.3 63.1 + - - +
75M ALA* 4.3 4.4 - - - +
76M GLN* 3.8 18.0 + - - +
82M LEU 5.1 5.1 + - - -
83M ARG* 5.2 1.4 - - - +
84M PHE* 4.3 50.3 + - + +
89M VAL* 5.1 5.1 - - - +
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Residues in contact with GLU 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 3.8 21.8 - - + +
23B ARG* 3.7 18.3 + - - -
24B ASP 4.2 3.6 + - - -
25B ASN* 2.3 53.6 + - - +
26B ILE* 5.3 1.2 + - - +
59B LYS* 4.4 12.6 + - - +
69M ARG 3.0 16.2 + - - +
70M LEU* 3.3 10.7 + - - +
72M ARG* 1.3 76.9 - - - +
74M ILE* 1.3 69.7 + - + +
76M GLN* 3.6 14.9 + - - +
77M ASP* 4.5 6.4 - - - +
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Residues in contact with ILE 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LYS* 4.4 31.9 - - + +
62B LEU* 4.2 32.8 - - + -
63B GLU* 4.2 20.9 - - + +
66B ILE* 3.9 17.7 - - + -
70M LEU* 3.0 35.5 + - + +
71M VAL* 3.9 3.8 - - - +
73M GLU* 1.3 75.9 - - + +
75M ALA* 1.3 59.1 + - - +
76M GLN 2.8 11.3 + - - -
77M ASP* 3.4 18.1 + - - +
78M PHE* 4.3 14.6 - - + -
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Residues in contact with ALA 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE* 3.7 28.3 - - + -
70B VAL* 5.2 4.9 - - + +
71M VAL 3.0 18.5 + - - +
72M ARG* 3.9 4.5 + - - +
73M GLU 3.4 0.4 - - - -
74M ILE* 1.3 75.4 - - - +
76M GLN* 1.3 58.1 + - - +
77M ASP 3.4 0.9 - - - -
78M PHE* 4.0 11.7 + - + +
79M LYS 3.5 15.1 + - - +
82M LEU* 4.1 11.9 - - + +
84M PHE* 4.1 24.2 - - + -
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Residues in contact with GLN 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS 4.8 2.8 + - - -
21B VAL* 4.0 33.6 - - - +
22B LEU* 4.2 24.5 + - - +
72M ARG 3.8 8.6 + - - +
73M GLU* 3.6 13.8 - - - +
74M ILE 2.8 1.6 + - - -
75M ALA* 1.3 75.8 - - - +
77M ASP* 1.3 63.9 + - - +
78M PHE 3.3 6.9 + - - -
79M LYS 4.2 11.0 + - - +
80M THR* 4.3 22.0 + - + +
81M ASP 5.6 3.2 - - - +
82M LEU* 5.8 0.7 - - - -
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Residues in contact with ASP 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M GLU 4.5 4.9 - - - +
74M ILE* 3.4 13.7 + - - +
76M GLN* 1.3 83.0 - - - +
78M PHE* 1.3 73.8 + - + +
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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