Contacts of the strand formed by residues 71 - 82 (chain D) in PDB entry 1NVP
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 VAL 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D ARG* 3.6 2.3 - - - +
67D PHE* 3.5 6.7 - - - -
68D CYS 2.8 28.5 + - - +
69D ASP* 3.5 15.3 - - + +
70D ASN* 1.3 80.3 - - - +
72D TRP* 1.3 70.0 + - - +
73D THR* 3.9 6.8 + - - +
96D VAL* 4.0 20.0 - - + -
97D ALA 3.5 9.4 - - - +
98D CYS* 3.9 25.4 - - + -
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Residues in contact with TRP 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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191A GLU* 3.7 21.8 - - + -
339C TYR* 3.6 23.7 - + + -
342C ILE* 3.6 30.4 - - + +
349C TRP* 3.6 33.2 - + - -
65D TYR* 4.2 10.8 - + - -
66D ARG 3.3 20.4 - - - -
67D PHE* 3.2 48.7 - + + -
71D VAL* 1.3 74.5 - - - +
73D THR* 1.3 60.5 + - - +
74D PHE* 3.4 36.1 - + + -
95D ILE 3.5 1.7 - - - +
96D VAL* 3.4 2.6 - - - -
97D ALA* 2.7 44.1 + - + +
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Residues in contact with THR 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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64D THR* 4.5 1.2 + - - -
65D TYR* 3.4 2.9 - - - -
66D ARG* 3.0 56.6 + - - +
71D VAL* 3.9 13.0 + - - +
72D TRP* 1.3 73.8 + - - +
74D PHE* 1.3 67.8 + - - +
75D VAL* 5.3 2.9 - - + -
94D LYS* 4.2 28.3 - - - +
95D ILE 3.2 7.2 - - - +
96D VAL* 4.4 10.8 - - + +
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Residues in contact with PHE 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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342C ILE* 3.9 16.6 - - + -
349C TRP* 4.1 7.4 - + - -
351C PHE* 3.5 42.2 - + - -
353C LEU* 5.4 1.8 - - + -
62D LEU* 3.9 5.6 - - + -
64D THR* 3.4 4.5 - - - +
65D TYR* 3.6 22.9 - - + -
72D TRP* 3.4 51.8 - + + -
73D THR* 1.3 74.4 - - - +
75D VAL* 1.3 73.3 + - - +
76D LEU* 3.7 17.0 - - + -
94D LYS* 3.4 5.0 - - - +
95D ILE* 2.8 53.1 + - + +
97D ALA* 5.3 2.9 - - + -
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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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188A ARG* 6.0 1.8 - - - +
62D LEU* 3.8 1.6 - - - +
63D ASN* 2.9 42.3 + - + +
64D THR* 3.2 27.1 + - - +
73D THR* 5.3 3.1 - - + -
74D PHE* 1.3 82.9 - - - +
76D LEU* 1.3 66.4 + - - +
77D ASN* 5.0 1.6 - - - +
92D LYS* 4.5 20.6 - - + -
93D VAL 3.3 10.1 - - - +
94D LYS* 4.3 20.4 - - + +
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Residues in contact with LEU 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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351C PHE* 4.6 9.0 - - + -
374C ALA* 3.3 34.3 - - + -
58D PHE* 4.6 14.6 - - + -
60D GLY* 4.2 8.5 - - - +
61D SER 3.3 15.3 - - - +
62D LEU* 3.7 16.2 - - + -
74D PHE* 3.7 16.4 - - + -
75D VAL* 1.3 81.7 - - - +
77D ASN* 1.3 64.2 + - - +
79D VAL* 3.3 20.6 - - + -
92D LYS* 3.3 4.7 - - - +
93D VAL* 2.9 36.2 + - + +
95D ILE* 4.2 14.6 - - + -
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Residues in contact with ASN 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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61D SER* 2.9 38.1 + - - +
63D ASN* 2.7 40.8 + - - +
75D VAL* 5.2 1.8 - - - +
76D LEU* 1.3 78.8 + - - +
78D ASP* 1.3 79.4 + - - +
79D VAL* 3.3 3.7 + - - +
91D ASP 3.1 15.3 + - - +
92D LYS* 3.8 13.3 - - - +
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Residues in contact with ASP 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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59D ARG 3.9 1.0 - - - +
60D GLY* 3.7 9.5 - - - -
61D SER* 5.2 3.6 + - - +
77D ASN* 1.3 80.7 - - - +
79D VAL* 1.3 62.6 + - - +
80D GLU* 5.3 2.4 - - - +
90D VAL 3.3 8.3 - - - -
91D ASP* 2.9 28.9 + - - +
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Residues in contact with VAL 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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58D PHE* 4.0 16.8 - - + -
59D ARG 3.2 18.4 - - - +
60D GLY* 4.6 0.9 - - - -
76D LEU* 3.3 39.7 - - + +
77D ASN 3.8 2.9 - - - +
78D ASP* 1.3 76.0 - - - +
80D GLU* 1.3 73.8 + - - +
81D PHE* 3.5 25.4 - - + -
89D LYS* 3.5 4.7 - - - +
90D VAL* 2.8 44.1 + - + +
93D VAL* 3.4 13.7 - - + +
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Residues in contact with GLU 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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57D ASN 4.2 0.3 - - - -
58D PHE* 3.2 20.6 - - - -
59D ARG* 2.9 19.7 + - + +
78D ASP 5.3 2.5 - - - +
79D VAL* 1.3 74.8 - - - +
81D PHE* 1.3 64.0 + - - +
82D ARG* 3.5 27.2 + - - +
87D LEU* 4.0 5.8 - - + +
88D ILE 3.5 3.6 - - - -
89D LYS* 3.3 46.8 + - + +
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Residues in contact with PHE 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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335C VAL* 4.4 5.2 - - + -
358C MET* 3.9 27.8 - - + -
360C LEU* 3.9 24.0 - - + -
56D VAL* 4.5 12.3 - - + -
57D ASN 3.3 4.7 - - - +
58D PHE* 3.6 27.6 - + + -
79D VAL* 3.5 24.2 - - + -
80D GLU* 1.3 71.4 - - - +
82D ARG* 1.3 60.8 + - - +
86D GLU 3.9 1.0 - - - +
87D LEU* 3.9 3.8 - - - +
88D ILE* 2.8 57.3 + - + +
90D VAL* 3.6 22.7 - - + -
93D VAL* 3.8 25.1 - - + -
95D ILE* 5.2 2.5 - - + -
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Residues in contact with ARG 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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55D ARG 4.5 0.2 - - - +
56D VAL* 3.5 6.3 - - - +
57D ASN* 2.4 70.6 + - + +
80D GLU* 3.5 21.0 + - - +
81D PHE* 1.3 67.9 + - - +
83D GLU* 1.3 65.5 + - - +
84D VAL* 5.0 2.2 - - - +
86D GLU* 4.3 6.7 - - - +
87D LEU* 3.3 40.2 - - - +
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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