Contacts of the helix formed by residues 64 - 75 (chain Q) in PDB entry 1NVU
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 TYR 64 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62Q GLU* 2.9 48.6 - - + -
63Q GLU* 1.3 79.2 - - + +
65Q SER* 1.3 64.6 + - - +
66Q ALA* 3.1 6.2 + - + +
67Q MET* 3.2 24.1 + - + +
68Q ARG* 3.2 23.6 + - + +
683S GLN* 3.6 37.7 - - + -
687S LEU* 3.5 28.7 - - + -
725S ALA* 4.1 13.8 + - + +
726S MET* 3.8 13.2 - - - +
729S TRP* 3.6 21.3 + + - -
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Residues in contact with SER 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q GLU 3.4 6.4 + - - -
64Q TYR* 1.3 75.7 - - - +
66Q ALA* 1.3 62.7 + - - +
68Q ARG* 3.4 18.2 + - - +
69Q ASP* 2.9 33.4 + - - +
99Q GLN* 4.8 3.1 - - - +
679S LYS* 4.4 17.5 - - - -
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Residues in contact with ALA 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Q TYR* 3.1 3.1 - - + +
65Q SER* 1.3 84.6 + - - +
67Q MET* 1.3 67.5 + - + +
69Q ASP* 3.7 13.7 + - - +
70Q GLN* 3.8 14.2 + - - +
73Q ARG* 5.4 0.2 + - - -
679S LYS* 3.6 32.1 - - + +
680S GLU* 5.0 10.8 - - + -
684S PRO* 5.7 1.8 - - + -
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Residues in contact with MET 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Q ILE* 4.9 4.5 - - + -
37Q GLU* 3.4 11.9 - - - +
64Q TYR* 3.2 16.6 + - + +
66Q ALA* 1.3 79.4 - - + +
68Q ARG* 1.3 56.5 - - - +
70Q GLN* 2.6 48.1 + - - +
71Q TYR* 3.5 20.4 + - + +
684S PRO* 3.9 28.7 - - + +
687S LEU* 3.8 30.7 - - + -
688S ARG* 3.1 50.3 - - + +
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Residues in contact with ARG 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q VAL* 6.2 0.7 - - - -
58Q THR* 5.7 3.1 - - - +
59Q GLY 4.1 17.0 + - - +
61Q GLN* 3.1 35.6 - - - +
62Q GLU* 3.3 9.5 - - - +
63Q GLU* 3.4 9.9 - - - +
64Q TYR* 3.2 10.9 + - + +
65Q SER* 3.4 33.5 - - - +
66Q ALA 3.4 0.2 - - - -
67Q MET* 1.3 75.5 - - - +
69Q ASP* 1.3 66.3 + - - +
71Q TYR* 2.8 33.7 + - + +
72Q MET* 3.4 17.9 + - + +
96Q TYR* 3.5 34.1 + - - -
99Q GLN* 3.5 24.2 + - - +
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Residues in contact with ASP 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Q SER* 2.9 15.8 + - - +
66Q ALA* 3.8 8.7 - - - +
67Q MET 3.2 0.4 - - - -
68Q ARG* 1.3 75.1 - - - +
70Q GLN* 1.3 62.5 + - - +
72Q MET* 3.3 10.2 + - - +
73Q ARG* 3.0 43.0 + - - +
99Q GLN* 2.5 32.7 + - - +
102Q ARG* 2.8 33.8 + - - -
103Q VAL* 3.4 14.5 - - + +
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Residues in contact with GLN 70 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Q ALA* 3.8 11.1 + - - +
67Q MET* 2.6 36.1 + - - +
69Q ASP* 1.3 73.2 - - - +
71Q TYR* 1.3 62.1 + - + +
73Q ARG* 3.7 29.9 + - - +
74Q THR* 4.4 8.5 + - - +
616S HIS 3.2 18.4 + - - -
617S MET* 3.3 21.0 + - - +
618S TYR* 3.0 15.9 - - + +
619S ALA* 4.6 6.3 + - - +
684S PRO* 5.1 2.0 - - - +
688S ARG* 2.8 39.2 + - - +
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Residues in contact with TYR 71 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q VAL* 3.9 14.1 - - + +
36Q ILE* 3.1 18.0 + - - +
37Q GLU* 2.8 41.6 + - + -
56Q LEU* 3.7 27.2 - - + +
58Q THR* 3.5 33.4 - - + -
59Q GLY 4.7 3.1 - - - -
67Q MET* 3.9 21.4 - - + +
68Q ARG* 2.8 44.0 + - + +
70Q GLN* 1.3 72.8 - - - +
72Q MET* 1.3 60.8 + - + +
74Q THR* 3.1 22.7 + - - -
75Q GLY 3.7 3.8 + - - -
619S ALA* 3.7 19.1 - - + -
688S ARG* 4.4 2.0 - - - -
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Residues in contact with MET 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q VAL* 4.5 18.4 - - + -
68Q ARG* 3.9 24.5 - - + +
69Q ASP 3.3 7.9 + - - +
71Q TYR* 1.3 78.5 - - + +
73Q ARG* 1.3 64.5 + - - +
74Q THR 3.3 0.4 - - - -
75Q GLY 3.8 1.0 + - - -
78Q PHE* 3.4 37.6 - - + -
96Q TYR* 4.6 6.3 - - + -
99Q GLN* 3.0 49.4 - - + +
100Q ILE* 3.8 23.6 - - + -
103Q VAL* 4.0 14.4 - - + -
104Q LYS* 3.3 18.3 + - + +
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Residues in contact with ARG 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69Q ASP* 3.0 43.9 + - - +
70Q GLN* 3.7 24.9 - - - +
71Q TYR 3.3 0.8 - - - -
72Q MET* 1.3 77.2 - - - +
74Q THR* 1.3 62.0 + - + +
103Q VAL* 3.8 24.2 + - + +
104Q LYS* 3.0 20.3 + - - +
617S MET 5.7 0.8 + - - -
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Residues in contact with THR 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q LYS* 3.8 24.9 - - - +
7Q VAL* 4.9 1.2 - - - +
56Q LEU* 4.8 8.7 - - - +
70Q GLN 4.6 9.4 + - - +
71Q TYR* 3.1 11.8 + - - -
73Q ARG* 1.3 80.2 - - + +
75Q GLY* 1.3 67.0 + - - +
76Q GLU* 3.7 4.2 + - - +
104Q LYS* 4.6 0.5 + - - -
597S GLY* 4.9 16.4 - - - +
598S ILE* 5.3 11.9 - - + -
619S ALA 6.1 1.3 - - - +
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Residues in contact with GLY 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q LYS* 3.8 7.6 - - - -
7Q VAL* 3.7 24.7 - - - -
71Q TYR 3.7 5.7 + - - -
72Q MET 3.8 0.8 + - - -
73Q ARG 3.6 1.0 - - - -
74Q THR* 1.3 83.8 + - - +
76Q GLU* 1.3 61.2 + - - +
77Q GLY 3.6 1.6 - - - -
78Q PHE* 4.2 7.9 - - - -
104Q LYS* 2.9 33.6 + - - +
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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