Contacts of the helix formed by residues 63 - 78 (chain A) in PDB entry 2Q7V
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 ALA 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A SER 4.6 1.1 - - - +
50A GLU* 3.3 19.5 - - - +
51A GLU* 3.6 7.0 + - - +
62A ILE* 1.3 77.4 - - - +
64A GLY* 1.3 65.2 + - - +
65A MET* 4.3 6.7 - - + +
66A GLU* 3.0 19.5 + - + +
67A LEU* 3.0 19.3 + - - +
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.0 45.7 - - - +
47A ALA* 4.1 0.9 - - - -
49A SER* 2.6 20.8 + - - -
52A VAL* 4.3 0.4 - - - +
62A ILE 3.5 2.4 + - - -
63A ALA* 1.3 69.7 - - - +
65A MET* 1.3 56.0 + - - +
67A LEU* 3.1 2.9 + - - +
68A ALA* 2.8 30.8 + - - +
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Residues in contact with MET 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A MET* 3.5 33.0 - - + -
42A PRO 5.5 1.8 - - - +
47A ALA* 3.2 39.1 + - + +
49A SER 4.2 1.0 + - - +
63A ALA* 3.2 6.7 - - + -
64A GLY* 1.3 76.2 - - - +
66A GLU* 1.3 56.4 + - - +
68A ALA* 3.8 6.4 - - + +
69A GLN* 3.0 48.7 + - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 3.7 23.6 - - + -
63A ALA* 3.0 20.0 + - + +
65A MET* 1.3 77.2 - - - +
67A LEU* 1.3 61.4 + - - +
69A GLN* 3.3 17.6 + - - +
70A ARG* 2.9 56.3 + - - +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.9 9.9 - - + -
52A VAL* 4.5 2.5 - - + -
55A PHE* 4.0 16.8 - - + -
58A PHE* 3.7 33.0 - - + -
62A ILE* 4.1 24.6 - - + +
63A ALA 3.0 12.2 + - - +
64A GLY* 3.6 8.5 - - - +
66A GLU* 1.3 78.2 - - - +
68A ALA* 1.3 59.9 + - - +
70A ARG* 3.4 4.4 + - - +
71A MET* 3.0 37.5 + - + +
293A LEU* 3.6 32.5 - - + -
57B GLY* 4.1 15.3 - - - +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.3 2.6 - - - +
42A PRO 4.3 5.8 - - - +
43A GLY* 3.4 28.2 - - - -
46A ILE* 4.1 9.1 - - + +
47A ALA* 4.7 6.3 - - + -
64A GLY 2.8 16.8 + - - +
65A MET* 3.8 9.2 - - + +
67A LEU* 1.3 74.1 - - - +
69A GLN* 1.3 59.6 + - - +
71A MET* 3.3 13.5 + - - +
72A HIS* 2.9 31.2 + - - +
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A MET* 6.1 2.6 - - - +
65A MET* 3.0 40.2 + - + +
66A GLU* 3.3 21.5 + - - +
68A ALA* 1.3 76.3 - - - +
70A ARG* 1.3 56.1 + - + +
72A HIS* 3.4 11.6 + - + +
73A GLN* 2.9 32.7 + - - +
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 3.7 17.6 - - - -
62A ILE* 3.8 21.1 - - - +
66A GLU* 2.9 41.7 + - - +
67A LEU* 3.7 4.9 - - - +
68A ALA 3.3 0.2 - - - -
69A GLN* 1.3 76.2 - - + +
71A MET* 1.3 56.5 + - - +
73A GLN* 3.4 4.8 + - - +
74A GLN* 2.9 30.5 + - - +
57B GLY* 2.8 31.9 + - - +
58B PHE* 3.6 18.8 - - - -
59B PRO* 3.7 26.9 - - + +
60B GLU* 3.4 28.7 + - - -
70B ARG* 4.9 2.6 - - - +
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Residues in contact with MET 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PRO* 3.5 50.7 - - + +
21A LEU* 3.8 18.0 - - + +
22A THR* 4.8 0.4 - - - -
25A ILE* 4.4 4.1 - - + +
43A GLY 4.9 0.2 - - - +
46A ILE* 4.3 7.9 - - + -
55A PHE* 5.8 3.1 - - - -
67A LEU* 3.0 32.8 + - + +
68A ALA* 3.7 14.8 - - + +
70A ARG* 1.3 74.2 - - - +
72A HIS* 1.3 57.8 + - - +
74A GLN* 3.4 4.4 + - - +
75A ALA* 3.0 29.5 + - - +
293A LEU* 4.9 3.4 - - + -
297A VAL* 4.6 3.6 - - - -
56B PRO* 4.2 17.7 - - + -
57B GLY* 3.6 24.7 - - - +
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Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.8 12.0 - - + +
42A PRO* 3.7 34.2 - - + +
68A ALA 2.9 17.7 + - - +
69A GLN* 3.6 11.2 - - + +
71A MET* 1.3 73.4 - - - +
73A GLN* 1.3 64.8 + - - +
75A ALA* 3.3 2.5 + - - +
76A GLU* 2.9 58.5 + - - +
82A VAL* 3.8 22.2 - - + +
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLN* 2.9 21.0 + - - +
70A ARG* 3.7 7.5 - - - +
72A HIS* 1.3 74.3 - - - +
74A GLN* 1.3 56.4 + - - +
76A GLU* 3.4 8.9 + - - +
77A LYS* 3.0 28.8 + - + +
59B PRO* 3.6 29.1 + - + +
60B GLU* 6.1 0.6 - - - +
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.5 17.4 - - + +
70A ARG 2.9 15.6 + - - +
71A MET 3.7 4.5 - - - +
72A HIS 3.3 0.2 - - - -
73A GLN* 1.3 72.7 - - - +
75A ALA* 1.3 66.0 + - - +
77A LYS* 3.3 18.6 + - - +
78A PHE* 3.3 21.8 - - + -
53B GLU 2.8 30.4 + - - +
54B ASN* 3.6 3.6 - - - +
55B PHE 2.9 25.2 + - - +
56B PRO* 3.5 1.4 - - - +
57B GLY* 2.9 29.3 + - - -
58B PHE 3.0 18.2 + - - -
59B PRO* 3.8 15.7 - - + +
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.6 34.8 - - + +
24A ALA* 4.0 15.0 - - + +
25A ILE* 3.7 11.6 - - - +
36A ILE* 4.4 5.2 - - + -
71A MET 3.0 16.7 + - - +
72A HIS 3.3 4.9 + - - +
74A GLN* 1.3 76.7 - - - +
76A GLU* 1.3 63.6 + - + +
77A LYS 3.3 0.3 + - - -
78A PHE* 3.4 10.6 + - - +
80A ALA* 3.7 19.1 + - - +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A HIS* 2.9 47.7 + - + +
73A GLN* 3.9 7.1 - - - +
75A ALA* 1.3 74.5 - - + +
77A LYS* 1.3 64.1 + - - +
78A PHE 3.3 0.7 + - - -
79A GLY* 3.3 10.2 + - - -
80A ALA 3.5 20.3 - - - +
81A LYS* 4.9 9.8 + - + +
82A VAL* 4.0 20.9 + - + +
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 3.0 15.1 + - + +
74A GLN 3.3 12.1 - - - +
75A ALA 3.2 0.4 - - - -
76A GLU* 1.3 78.5 - - - +
78A PHE* 1.3 87.5 + - + +
79A GLY 3.6 0.7 + - - -
53B GLU* 3.9 20.4 + - - +
58B PHE 5.2 0.2 + - - -
59B PRO* 2.9 35.3 + - + +
61B PRO* 3.8 19.8 - - - +
148B PHE* 5.9 0.3 - - - -
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.9 17.5 - - + +
28A GLY* 3.0 25.6 - - - +
29A ARG* 3.5 40.2 - - + +
31A GLN* 5.2 0.9 + - - -
74A GLN* 3.3 28.3 - - + -
75A ALA 3.4 7.5 + - - +
76A GLU 3.2 0.6 - - - -
77A LYS* 1.3 104.6 - - + +
79A GLY* 1.3 56.8 + - - +
80A ALA 3.7 2.5 - - - -
53B GLU* 3.4 50.9 - - + -
148B PHE* 3.8 36.3 - + - -
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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