Contacts of the helix formed by residues 68 - 77 (chain D) in PDB entry 1NBI
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 GLY 68 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D CYS* 2.8 31.0 + - - -
66D GLY 2.9 0.2 - - - -
67D THR* 1.3 79.7 + - - +
69D VAL* 1.3 57.1 + - - +
70D ASP 3.4 2.0 - - - -
71D SER* 3.1 6.3 + - - -
72D ILE* 2.6 44.8 + - - +
94D ALA* 4.1 4.7 - - - -
110D TRP* 4.4 1.6 - - - -
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Residues in contact with VAL 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ILE* 3.8 17.3 - - + -
37D THR* 4.1 23.6 - - + -
40D ARG* 3.9 34.5 - - + +
41D THR* 5.0 6.4 + - - +
65D CYS 4.3 1.2 + - - -
67D THR* 3.5 20.9 + - - +
68D GLY* 1.3 78.2 - - - +
70D ASP* 1.3 69.3 + - - +
72D ILE* 3.5 9.7 - - - +
73D MET* 3.3 18.4 + - - +
3293D SAM 4.3 9.4 + - - +
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Residues in contact with ASP 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 3.6 12.0 + - - -
41D THR* 4.7 1.0 + - - -
44D TYR* 2.9 39.9 + - - -
48D LEU* 4.7 7.0 - - + -
62D ASP* 4.5 9.2 + - - +
65D CYS 5.4 0.6 + - - +
68D GLY 3.4 0.2 - - - -
69D VAL* 1.3 85.3 - - - +
71D SER* 1.3 62.6 + - - +
73D MET* 3.5 16.4 + - - +
74D LEU* 3.4 27.5 + - - +
134D ILE* 4.9 9.6 - - + -
136D LEU* 3.7 23.8 - - + +
3293D SAM 4.8 6.8 + - - +
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Residues in contact with SER 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ASP* 3.4 22.6 + - - +
65D CYS* 4.5 0.9 - - - -
68D GLY* 3.1 9.3 + - - -
70D ASP* 1.3 76.2 - - - +
72D ILE* 1.3 66.9 + - - +
74D LEU* 3.5 6.4 + - - +
75D VAL* 3.1 23.4 + - - +
81D VAL* 3.3 15.4 - - - +
83D SER* 2.6 32.2 + - - -
110D TRP* 3.6 16.4 - - - -
134D ILE* 5.9 0.7 - - - -
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Residues in contact with ILE 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D THR 4.4 4.7 - - - +
68D GLY* 2.6 34.7 + - - +
69D VAL* 3.5 8.7 - - + +
71D SER* 1.3 72.3 - - - +
73D MET* 1.3 52.9 + - - +
75D VAL* 2.9 9.7 + - - +
76D GLU* 2.7 56.2 + - - +
97D GLU* 3.9 26.2 - - + +
101D ARG* 4.2 4.7 - - - +
107D PHE* 3.9 12.1 - - + -
110D TRP* 3.2 29.4 - - + -
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Residues in contact with MET 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D THR* 3.0 31.4 - - + +
44D TYR* 4.7 6.5 - - + -
45D LYS* 3.5 37.5 - - + +
48D LEU* 5.3 2.7 - - + -
49D LEU* 3.2 31.9 - - + -
69D VAL 3.3 8.6 + - - +
70D ASP* 3.6 21.5 - - - +
71D SER 3.3 0.4 - - - -
72D ILE* 1.3 77.6 - - - +
74D LEU* 1.3 66.8 + - + +
76D GLU* 2.5 39.7 + - + +
77D GLU* 2.5 22.3 + - + +
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 4.5 9.6 - - + -
49D LEU* 4.1 12.6 - - + -
52D LEU* 3.6 30.7 - - + -
60D VAL* 3.9 19.5 - - + -
70D ASP 3.4 14.2 + - - +
71D SER* 3.8 8.1 - - - +
73D MET* 1.3 98.5 - - - +
75D VAL* 1.3 64.0 + - - +
77D GLU* 3.0 6.0 + - - -
79D PHE* 2.8 47.5 + - + -
81D VAL* 4.5 6.1 - - + -
134D ILE* 3.9 22.9 - - + -
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Residues in contact with VAL 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D SER 3.1 11.9 + - - +
72D ILE* 2.9 11.2 + - - +
73D MET 2.7 4.0 + - - -
74D LEU* 1.3 73.9 - - - +
76D GLU* 1.3 58.8 + - - +
78D GLY* 2.9 21.0 + - - -
79D PHE 3.8 5.8 + - - +
81D VAL* 3.0 30.1 - - + -
106D ALA* 4.0 22.3 - - + +
107D PHE* 3.5 42.0 - - + +
110D TRP* 3.9 31.4 - - + -
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Residues in contact with GLU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ILE* 2.7 22.8 + - + +
73D MET* 2.5 21.3 + - + +
75D VAL* 1.3 74.3 - - - +
77D GLU* 1.3 59.3 + - + +
78D GLY 3.1 4.5 + - - -
101D ARG* 2.5 49.6 + - - +
106D ALA* 5.7 1.3 - - - -
107D PHE* 4.1 4.9 - - + -
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LYS* 3.3 25.8 + - - -
49D LEU* 3.8 19.5 - - + -
53D ARG* 4.0 13.3 + - - +
73D MET* 2.5 33.2 + - + +
74D LEU* 3.0 4.2 + - - -
76D GLU* 1.3 77.9 - - + +
78D GLY* 1.3 59.1 + - - +
79D PHE* 2.9 33.9 - - + -
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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