Contacts of the helix formed by residues 64 - 78 (chain A) in PDB entry 1NN3
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 GLU 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A VAL* 1.3 75.2 - - - +
65A ASP* 1.3 63.1 + - - +
66A HIS* 2.7 49.8 + - - +
67A SER* 2.9 22.9 + - - -
68A VAL* 2.9 26.3 + - - +
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Residues in contact with ASP 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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56A TYR* 3.8 6.2 + - - -
63A VAL 3.4 3.9 + - - +
64A GLU* 1.3 77.3 + - - +
66A HIS* 1.3 63.8 + - + +
68A VAL* 3.4 7.9 - - - +
69A HIS* 3.2 22.2 + - - +
106A THR* 4.7 1.4 - - - +
109A LYS* 2.8 41.1 + - + +
112A PHE* 3.6 27.0 - - + -
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Residues in contact with HIS 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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64A GLU* 2.7 34.7 + - - +
65A ASP* 1.3 71.3 - - + +
67A SER* 1.3 68.2 + - - +
69A HIS* 3.2 3.3 + - - +
70A LEU* 3.0 31.6 + - + +
111A ASN 5.1 4.6 + - - -
112A PHE* 3.4 36.0 - + - -
116A TRP* 3.7 33.6 - + + -
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Residues in contact with SER 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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63A VAL* 3.8 14.3 - - - +
64A GLU* 2.9 24.3 + - - -
66A HIS* 1.3 76.9 - - - +
68A VAL* 1.3 63.1 + - - +
70A LEU* 3.2 11.7 + - - +
71A LEU* 2.9 31.2 + - - +
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Residues in contact with VAL 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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52A LEU 5.8 0.2 - - - +
53A LEU* 3.7 19.7 - - + -
56A TYR* 3.6 53.6 - - + +
63A VAL* 3.6 20.6 - - + +
64A GLU 2.9 10.6 + - - +
65A ASP* 3.4 15.5 - - - +
67A SER* 1.3 77.3 - - - +
69A HIS* 1.3 67.4 + - + +
71A LEU* 3.2 6.0 + - + +
72A PHE* 2.9 34.2 + - + -
106A THR* 5.5 1.6 - - - +
109A LYS* 4.1 6.1 - - - +
151A TYR* 4.7 2.0 - - - +
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Residues in contact with HIS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP 3.2 10.7 + - - +
66A HIS 3.4 9.2 - - - +
68A VAL* 1.3 80.4 - - - +
70A LEU* 1.3 65.0 + - + +
72A PHE* 3.2 11.8 + - - +
73A SER* 3.1 20.3 + - - -
76A ARG* 5.1 4.2 + - - -
102A GLY* 3.4 26.5 + - - -
106A THR* 2.8 34.8 + - + +
116A TRP* 3.4 27.4 - + + -
117A CYS* 2.8 39.3 + - + -
120A PRO* 4.0 14.9 - - + +
121A ASP* 5.6 1.5 + - - -
301A 2DT 6.2 0.2 + - - -
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Residues in contact with LEU 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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66A HIS* 3.0 22.6 + - + +
67A SER* 3.6 10.1 - - - +
69A HIS* 1.3 74.7 - - + +
71A LEU* 1.3 60.9 + - + +
73A SER* 3.2 5.1 + - - +
74A ALA* 2.8 30.1 + - - +
116A TRP* 4.2 22.0 - - + -
120A PRO* 3.6 32.1 - - + -
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Residues in contact with LEU 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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49A ILE* 3.4 26.2 - - + +
52A LEU* 4.1 35.2 - - + -
53A LEU* 3.6 15.5 - - + -
63A VAL* 4.6 11.0 - - + -
67A SER* 2.9 28.6 + - - +
68A VAL* 3.5 13.7 - - + +
70A LEU* 1.3 73.4 - - + +
72A PHE* 1.4 62.2 + - - +
74A ALA* 3.2 5.2 + - + +
75A ASN* 2.9 31.7 + - - +
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Residues in contact with PHE 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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43A PRO* 4.0 24.5 - - + -
53A LEU* 3.7 30.3 - - + -
56A TYR* 4.6 9.0 - + - -
57A LEU* 4.1 18.6 - - + -
68A VAL* 2.9 39.7 + - + -
69A HIS* 3.2 11.4 + - - +
71A LEU* 1.4 80.2 - - - +
73A SER* 1.3 60.8 + - - +
75A ASN* 3.4 13.2 - - - +
76A ARG* 3.4 20.0 + - - +
102A GLY* 5.4 1.1 - - - -
106A THR* 5.5 2.5 - - - -
151A TYR* 4.8 1.6 - - - -
301A 2DT 3.2 72.5 - + + +
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Residues in contact with SER 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 HIS* 3.1 13.6 + - - -
70A LEU 3.7 6.1 - - - -
71A LEU 3.2 0.2 - - - -
72A PHE* 1.3 76.1 - - - +
74A ALA* 1.3 66.2 + - - +
76A ARG* 2.9 28.0 + - - +
77A TRP* 3.0 18.8 + - - -
120A PRO* 3.3 39.0 + - - +
121A ASP* 2.7 22.5 + - - -
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Residues in contact with ALA 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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49A ILE* 3.8 22.7 - - + +
70A LEU 2.8 20.5 + - - +
71A LEU* 3.7 8.7 - - + +
73A SER* 1.3 71.8 - - - +
75A ASN* 1.3 56.3 - - - +
77A TRP* 3.2 11.2 + - - +
78A GLU* 2.9 31.7 + - - +
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Residues in contact with ASN 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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42A PHE* 3.6 13.4 - - - -
43A PRO* 3.2 13.0 - - - +
44A GLU* 2.8 51.0 + - - +
47A THR* 3.4 5.5 + - - -
49A ILE* 3.9 3.7 - - + +
50A GLY 3.8 4.9 - - - +
53A LEU* 3.8 12.7 - - + +
71A LEU 2.9 17.1 + - - +
72A PHE 3.4 8.0 - - - +
73A SER 3.1 0.2 - - - -
74A ALA* 1.3 77.8 - - - +
76A ARG* 1.3 59.3 + - - +
78A GLU* 2.9 42.3 + - - +
79A GLN* 3.7 3.1 - - - +
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Residues in contact with ARG 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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42A PHE* 3.6 32.6 - - + +
69A HIS* 5.1 3.4 + - - -
72A PHE* 3.4 14.1 + - - +
73A SER* 2.9 20.4 + - - +
75A ASN* 1.3 77.9 - - - +
77A TRP* 1.3 65.3 + - - +
79A GLN* 2.9 16.8 + - - +
80A VAL* 3.4 12.9 + - - +
83A ILE* 4.8 1.4 - - - +
98A TYR* 3.7 14.7 + - + +
99A ALA* 3.7 23.4 - - - +
102A GLY* 3.9 9.3 - - - -
121A ASP* 2.9 41.9 + - - -
124A LEU* 3.9 19.5 - - + -
301A 2DT 2.8 42.4 + - - +
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Residues in contact with TRP 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 SER* 3.0 33.3 + - - -
74A ALA* 3.2 10.5 + - - +
76A ARG* 1.3 74.9 - - - +
78A GLU* 1.3 62.1 + - - +
80A VAL* 3.0 44.6 + - + +
81A PRO* 3.6 5.7 - - - +
84A LYS* 6.3 0.7 - - - -
120A PRO 2.8 22.3 + - - -
121A ASP* 4.2 0.6 - - - +
122A VAL 3.4 21.5 - - - -
123A GLY* 3.5 26.5 - - - -
124A LEU* 3.5 23.1 - - + +
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Residues in contact with GLU 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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47A THR* 2.7 40.3 + - - +
49A ILE* 3.8 19.2 + - + +
74A ALA 2.9 11.9 + - - +
75A ASN* 2.9 35.8 + - - +
77A TRP* 1.3 76.4 - - - +
79A GLN* 1.3 69.9 + - - +
81A PRO* 3.7 10.5 - - - +
82A LEU* 5.3 0.7 + - - +
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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