Contacts of the helix formed by residues 74 - 92 (chain D) in PDB entry 2NS7
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 SER 74 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D GLY 4.0 2.2 + - - -
73D GLU* 1.3 75.8 - - - +
75D TRP* 1.3 60.4 + - - +
76D GLN* 3.5 16.9 + - - +
77D ASP* 3.1 33.0 + - - +
78D PHE* 2.9 26.5 + - - +
119D PHE* 4.3 0.2 - - - -
123D GLN* 5.5 3.8 - - - +
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Residues in contact with TRP 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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73D GLU 3.8 1.8 + - - -
74D SER* 1.3 72.9 - - - +
76D GLN* 1.3 91.3 + - + +
78D PHE* 3.9 1.8 - - - +
79D LEU* 3.0 57.3 + - + +
119D PHE* 3.7 29.6 - - + -
120D LEU* 3.8 11.4 - - + -
123D GLN* 3.6 34.2 + - + +
125D PHE* 3.7 22.8 - + - -
194D ILE* 4.1 5.4 - - + -
197D PHE* 3.5 33.2 - + + -
198D GLU* 3.6 26.9 - - + -
201D LEU* 4.6 10.0 - - + +
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Residues in contact with GLN 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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74D SER* 3.5 19.2 - - - +
75D TRP* 1.3 114.7 + - + +
77D ASP* 1.3 64.1 + - - +
79D LEU 3.3 0.9 + - - -
80D ARG* 3.0 48.7 + - - +
194D ILE* 3.5 30.7 - - + +
198D GLU* 2.8 26.5 + - - +
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Residues in contact with ASP 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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73D GLU* 3.5 19.2 - - + +
74D SER* 3.0 26.4 + - - +
76D GLN* 1.3 77.7 - - - +
78D PHE* 1.3 56.1 + - - +
80D ARG* 3.0 26.7 + - - +
81D ASN* 2.7 41.3 + - - +
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Residues in contact with PHE 78 (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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66D HIS* 3.8 8.5 - + - -
67D PHE 3.6 21.1 - - - -
68D SER* 3.5 23.8 - - - -
69D PRO* 3.7 15.7 - - + -
73D GLU* 3.4 17.4 - - + +
74D SER 2.9 14.7 + - - +
75D TRP 4.0 2.9 - - - +
77D ASP* 1.3 74.3 - - - +
79D LEU* 1.3 80.7 + - + +
82D ASN* 2.8 53.2 + - + +
116D GLN* 3.6 29.2 - - + -
119D PHE* 3.9 31.0 - + + -
120D LEU* 5.1 2.2 - - + -
134D LEU* 4.6 4.5 - - + -
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Residues in contact with LEU 79 (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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75D TRP* 3.0 48.6 + - + +
76D GLN 3.3 3.8 + - - +
78D PHE* 1.3 97.6 - - + +
80D ARG* 1.3 63.6 + - - +
82D ASN* 3.8 5.1 - - - +
83D ALA* 3.0 24.4 + - - +
120D LEU* 4.5 13.5 - - + -
125D PHE* 5.0 1.6 - - + -
133D ALA* 5.1 2.9 - - + -
134D LEU* 4.2 20.6 - - + +
137D VAL* 4.4 23.1 - - + +
190D LEU* 4.9 1.8 - - + -
194D ILE* 4.1 12.3 - - + -
197D PHE* 3.9 20.2 - - + -
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Residues in contact with ARG 80 (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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76D GLN* 3.0 46.2 + - - +
77D ASP* 3.0 31.1 + - - +
79D LEU* 1.3 75.8 - - - +
81D ASN* 1.3 59.5 + - - +
83D ALA* 3.1 4.2 + - - +
84D LYS* 2.8 53.6 + - - +
190D LEU* 4.0 15.3 - - + +
191D GLU* 2.9 39.9 + - - +
194D ILE* 3.4 15.3 - - + +
195D ARG* 4.1 20.2 - - - +
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Residues in contact with ASN 81 (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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66D HIS* 3.4 32.4 - - + +
70D LEU* 5.8 0.2 - - - +
73D GLU* 2.8 17.4 + - - -
77D ASP* 2.7 28.7 + - - +
80D ARG* 1.3 77.0 - - - +
82D ASN* 1.3 60.2 + - - +
84D LYS* 3.8 20.7 + - - +
85D SER* 2.9 30.8 + - - -
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Residues in contact with ASN 82 (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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64D HIS* 3.2 30.0 + - - -
66D HIS* 2.8 30.1 + - - +
67D PHE* 3.4 11.3 - - - +
78D PHE* 2.8 35.0 + - + +
79D LEU* 3.8 6.6 - - - +
81D ASN* 1.3 77.4 - - - +
83D ALA* 1.3 57.3 + - - +
85D SER* 4.2 0.2 - - - -
86D PHE* 2.9 25.3 + - - +
116D GLN* 3.5 15.2 + - - +
134D LEU* 5.0 6.9 - - - +
137D VAL* 5.5 4.3 - - - +
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Residues in contact with ALA 83 (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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79D LEU 3.0 18.6 + - - +
80D ARG 3.5 3.8 - - - +
82D ASN* 1.3 75.3 + - - +
84D LYS* 1.3 66.2 + - - +
86D PHE* 3.3 6.1 + - - +
87D ARG* 2.9 24.8 + - - +
137D VAL* 3.7 24.5 - - + -
141D THR* 3.7 15.7 - - - +
186D PHE* 4.1 2.5 - - + -
190D LEU* 3.9 17.9 - - + -
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Residues in contact with LYS 84 (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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80D ARG* 2.8 47.9 + - - +
81D ASN* 3.8 18.4 + - - +
83D ALA* 1.3 71.7 - - - +
85D SER* 1.3 58.4 + - - +
87D ARG* 3.3 4.1 + - - +
88D ASN* 2.9 38.5 + - - +
186D PHE* 4.2 21.5 - - + -
187D LEU* 3.9 23.3 - - + -
190D LEU* 4.6 4.9 - - + -
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Residues in contact with SER 85 (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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63D HIS 3.5 9.6 + - - +
64D HIS* 2.6 29.2 + - - -
65D THR* 2.8 23.4 + - - -
66D HIS* 3.0 14.0 + - - -
81D ASN 2.9 19.8 + - - -
82D ASN 3.6 2.5 - - - -
84D LYS* 1.3 74.9 - - - +
86D PHE* 1.3 66.2 + - - +
88D ASN* 3.3 9.3 + - - +
89D ALA 3.2 15.1 + - - -
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Residues in contact with PHE 86 (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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60D LEU* 4.0 16.8 - - + -
64D HIS* 3.4 19.2 + + + +
82D ASN* 2.9 19.9 + - - +
83D ALA* 3.6 6.5 - - - +
85D SER* 1.3 73.4 - - - +
87D ARG* 1.3 63.2 + - - +
89D ALA* 3.1 15.2 + - - +
90D LEU* 3.2 36.7 + - + +
100D HIS* 3.6 39.9 - + - -
138D GLY* 3.6 31.0 - - - -
141D THR* 3.6 21.8 - - + -
142D LEU* 4.3 5.8 - - + -
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Residues in contact with ARG 87 (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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83D ALA 2.9 12.8 + - - +
84D LYS* 3.4 9.3 - - - +
86D PHE* 1.3 76.7 - - - +
88D ASN* 1.3 64.4 + - - +
90D LEU* 3.1 4.2 + - - +
91D LEU* 2.9 55.7 + - + +
141D THR* 3.7 14.1 - - + +
144D SER* 4.7 3.0 + - - -
145D VAL* 3.7 22.0 - - + +
148D ASP* 4.0 15.0 + - - +
182D ALA* 4.4 2.4 + - - +
183D GLU* 3.4 55.1 + - - +
186D PHE* 3.7 40.6 - - + +
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Residues in contact with ASN 88 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D HIS* 4.2 13.4 + - + +
84D LYS* 2.9 26.1 + - - +
85D SER* 3.3 12.4 + - - +
87D ARG* 1.3 82.1 - - - +
89D ALA* 1.3 62.2 + - - +
91D LEU* 3.4 13.7 + - - +
92D SER* 3.1 23.6 + - - -
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Residues in contact with ALA 89 (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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59D MET* 2.9 39.7 - - + +
60D LEU* 4.3 10.1 - - + +
63D HIS* 3.5 15.4 - - + +
64D HIS* 3.9 13.5 - - + +
85D SER 3.2 6.9 + - - +
86D PHE 3.1 11.5 + - - +
88D ASN* 1.3 79.2 - - - +
90D LEU* 1.3 58.0 + - + +
92D SER* 2.6 22.9 + - - -
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Residues in contact with LEU 90 (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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59D MET* 3.7 5.5 - - + +
60D LEU* 5.5 1.3 - - + -
86D PHE* 3.2 45.1 + - + +
87D ARG* 3.1 8.4 + - - +
89D ALA* 1.3 79.0 - - + +
91D LEU* 1.3 56.4 + - - +
92D SER 3.3 0.9 + - - -
93D HIS 3.6 0.9 - - - +
96D GLY* 3.2 20.2 - - - +
97D ALA* 4.0 5.2 - - - +
100D HIS* 3.6 39.0 - - + +
141D THR 4.4 0.9 - - - +
142D LEU* 4.1 17.9 - - + -
145D VAL* 3.9 30.3 - - + -
149D GLN* 2.8 23.6 + - - -
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Residues in contact with LEU 91 (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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87D ARG* 2.9 60.3 + - + +
88D ASN* 3.8 12.6 - - - +
90D LEU* 1.3 76.5 - - - +
92D SER* 1.3 61.5 + - - +
93D HIS 3.3 5.8 + - - +
145D VAL* 4.1 16.6 - - + -
148D ASP* 3.5 25.4 - - - +
149D GLN* 3.6 8.7 + - + +
152D GLN* 4.4 9.4 - - - +
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Residues in contact with SER 92 (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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18D ASN* 4.9 1.9 + - - +
59D MET* 3.2 8.8 - - - +
63D HIS* 3.5 31.8 - - - -
88D ASN 3.1 11.5 + - - -
89D ALA 2.6 20.3 + - - -
90D LEU 3.2 1.2 - - - -
91D LEU* 1.3 78.3 - - - +
93D HIS* 1.3 84.0 + - - +
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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