Contacts of the helix formed by residues 63 - 78 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B SER 4.7 1.1 - - - +
50B GLU 3.4 20.0 - - - +
51B GLU* 3.5 7.5 + - - +
52B VAL* 4.7 0.2 - - - -
62B ILE* 1.3 75.5 - - - +
64B GLY* 1.3 61.3 + - - +
65B MET* 4.3 7.9 - - + +
66B GLU* 3.0 18.7 + - + +
67B LEU* 2.9 26.3 + - - +
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.1 30.8 - - - +
47B ALA* 4.1 1.3 - - - -
49B SER 2.9 17.8 + - - -
52B VAL* 4.0 15.6 - - - +
62B ILE 3.5 2.4 + - - -
63B ALA* 1.3 70.8 - - - +
65B MET* 1.3 55.3 + - - +
67B LEU* 3.3 3.4 + - - +
68B ALA* 2.9 31.9 + - - +
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Residues in contact with MET 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ALA* 3.3 30.0 + - + +
49B SER 4.2 1.5 + - - +
63B ALA* 3.2 6.9 - - + +
64B GLY* 1.3 76.1 - - - +
66B GLU* 1.3 57.0 + - + +
68B ALA* 3.5 4.4 + - - +
69B GLN* 3.0 28.3 + - - +
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ILE* 4.0 18.4 - - + -
63B ALA* 3.0 19.4 + - + +
65B MET* 1.3 76.5 - - - +
67B LEU* 1.3 67.2 + - - +
69B GLN* 3.4 14.6 + - - +
70B ARG* 3.1 51.3 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY* 4.0 15.9 - - - +
46B ILE* 4.6 6.3 - - + -
52B VAL* 4.5 13.5 - - + -
55B PHE* 4.1 11.7 - - + -
58B PHE* 3.8 33.7 - - + -
62B ILE* 3.9 18.9 - - + +
63B ALA 2.9 15.6 + - - +
64B GLY* 3.8 5.2 - - - +
66B GLU* 1.3 74.9 - - - +
68B ALA* 1.3 58.2 + - - +
70B ARG* 3.3 4.5 + - - +
71B MET* 3.0 48.8 + - + +
293B LEU* 3.7 30.7 - - + -
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.2 3.8 - - - +
41B MET* 5.3 0.7 - - - -
42B PRO 4.3 5.6 - - - +
43B GLY* 3.6 29.7 - - - -
46B ILE* 4.1 11.2 - - + +
47B ALA* 4.9 5.8 - - + +
64B GLY 2.9 18.8 + - - +
65B MET* 3.6 7.0 - - - +
66B GLU 3.2 0.2 - - - -
67B LEU* 1.3 76.6 - - - +
69B GLN* 1.3 56.6 + - - +
71B MET* 3.3 9.1 + - - +
72B HIS* 2.9 29.2 + - - +
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B MET 3.0 18.1 + - - +
66B GLU* 3.7 18.6 - - - +
68B ALA* 1.3 76.3 - - - +
70B ARG* 1.3 66.8 + - - +
72B HIS* 3.2 12.5 + - + +
73B GLN* 2.9 57.2 + - - +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLY* 2.9 31.6 + - - +
58A PHE* 3.8 20.0 - - - +
59A PRO* 3.5 30.7 - - + +
70A ARG* 4.9 2.6 - - - +
58B PHE* 3.7 20.1 - - - -
62B ILE* 3.8 21.4 - - - +
66B GLU* 3.1 41.4 + - - +
67B LEU* 3.3 5.1 + - - +
69B GLN* 1.3 83.7 - - - +
71B MET* 1.3 56.0 + - - +
73B GLN* 3.5 1.3 + - - +
74B GLN* 3.1 27.9 + - - +
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Residues in contact with MET 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 4.1 17.9 - - + +
57A GLY* 3.8 15.7 - - - +
18B PRO* 4.0 34.5 - - + +
21B LEU* 3.8 18.6 - - + +
22B THR* 4.9 0.7 - - - +
25B ILE* 4.5 4.5 - - + +
46B ILE* 5.8 0.9 - - - -
55B PHE* 4.0 28.3 - - + -
67B LEU* 3.0 42.7 + - + +
68B ALA* 3.3 9.4 + - - +
70B ARG* 1.3 72.8 - - - +
72B HIS* 1.3 59.6 + - - +
74B GLN* 3.4 6.3 + - - +
75B ALA* 3.0 29.1 + - - +
293B LEU* 4.7 4.3 - - + -
297B VAL* 4.2 7.2 - - + -
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Residues in contact with HIS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.8 12.7 - - + +
42B PRO* 3.7 37.9 - - + +
68B ALA 2.9 14.4 + - - +
69B GLN* 3.2 17.0 + - + +
71B MET* 1.3 73.8 - - - +
73B GLN* 1.3 65.4 + - - +
75B ALA* 3.3 2.8 + - - +
76B GLU* 2.9 57.1 + - - +
82B VAL* 3.7 20.3 - - + +
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 3.9 27.7 + - + +
60A GLU* 5.1 7.5 - - - +
69B GLN* 2.9 42.2 + - - +
70B ARG* 3.8 5.5 - - - +
72B HIS* 1.3 77.1 - - - +
74B GLN* 1.3 56.7 + - - +
76B GLU* 3.3 8.8 + - - +
77B LYS* 2.9 30.1 + - + +
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU 2.8 28.7 + - - +
54A ASN* 3.6 4.0 - - - +
55A PHE 2.9 26.2 + - - +
56A PRO* 3.6 0.7 - - - +
57A GLY* 2.9 28.9 + - - -
58A PHE 3.0 17.3 + - - +
59A PRO* 3.8 17.2 - - + +
25B ILE* 3.5 17.1 - - + +
70B ARG 3.1 14.5 + - - +
71B MET 3.8 4.7 - - - +
72B HIS 3.3 0.2 - - - -
73B GLN* 1.3 78.5 - - - +
75B ALA* 1.3 61.0 + - - +
77B LYS* 3.4 9.5 - - + +
78B PHE* 3.2 34.3 - - + -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.6 35.7 - - + +
24B ALA* 4.1 12.6 - - + +
25B ILE* 3.8 11.8 - - - +
36B ILE* 4.3 4.7 - - + -
71B MET 3.0 18.1 + - - +
72B HIS 3.6 4.5 - - - +
73B GLN 3.3 0.2 - - - -
74B GLN* 1.3 73.0 - - - +
76B GLU* 1.3 65.9 + - + +
77B LYS 3.4 0.3 + - - -
78B PHE* 3.5 10.4 + - - +
79B GLY 3.8 0.2 + - - -
80B ALA* 3.5 21.4 + - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B HIS* 2.9 49.4 + - + +
73B GLN* 3.9 6.9 - - - +
75B ALA* 1.3 73.9 - - - +
77B LYS* 1.3 66.1 + - - +
79B GLY* 3.1 15.1 + - - -
80B ALA 3.7 18.5 - - - +
81B LYS* 5.5 0.2 - - - -
82B VAL* 3.5 20.6 + - + +
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.9 11.6 + - - +
58A PHE 5.1 1.4 + - - -
59A PRO* 2.9 34.3 + - + +
61A PRO* 3.5 29.1 - - - +
73B GLN* 2.9 15.3 + - + +
74B GLN* 3.4 10.8 - - - +
75B ALA 3.3 0.4 - - - -
76B GLU* 1.3 77.5 - - - +
78B PHE* 1.3 92.3 + - + +
79B GLY 3.3 0.9 + - - -
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 3.5 54.3 - - + -
148A PHE* 3.9 22.6 - + - -
25B ILE* 3.9 20.4 - - + +
28B GLY* 3.2 25.2 - - - +
29B ARG* 3.7 40.2 - - + +
74B GLN* 3.2 29.2 - - + +
75B ALA 3.5 5.9 + - - +
76B GLU 3.2 0.8 - - - -
77B LYS* 1.3 110.8 - - + +
79B GLY* 1.3 56.0 + - - +
80B ALA 3.6 2.7 - - - -
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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