Contacts of the strand formed by residues 87 - 98 (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 LEU 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D GLU* 4.0 8.1 - - + +
81D PHE 4.0 4.3 - - - +
82D ARG* 3.3 28.4 - - - +
86D GLU* 1.3 76.0 - - + +
88D ILE* 1.3 73.0 + - - +
89D LYS* 3.2 51.6 - - + +
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Residues in contact with ILE 88 (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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358C MET* 6.0 1.6 - - + -
360C LEU* 3.7 30.5 - - + -
361C ASN* 3.7 20.9 - - - +
365C TYR* 3.4 44.9 - - + +
79D VAL 3.9 0.5 - - - +
80D GLU* 3.5 2.8 - - - -
81D PHE* 2.8 53.6 + - + +
83D GLU* 5.2 9.4 - - + +
86D GLU 4.4 5.6 - - - +
87D LEU* 1.3 81.8 - - - +
89D LYS* 1.3 63.6 + - - +
90D VAL* 5.8 0.4 - - + -
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Residues in contact with LYS 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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361C ASN* 3.3 22.2 + - - +
79D VAL 3.5 4.0 - - - +
80D GLU* 3.3 34.1 + - + +
87D LEU* 3.2 47.6 - - + +
88D ILE* 1.3 73.2 - - - +
90D VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 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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333C ASN* 3.0 28.9 - - + +
360C LEU* 5.0 5.2 - - + -
361C ASN* 4.4 9.2 - - - +
78D ASP* 3.3 2.9 - - - -
79D VAL* 2.8 49.8 + - + +
81D PHE* 3.6 31.9 - - + -
88D ILE* 5.8 0.2 - - + -
89D LYS* 1.3 76.2 - - - +
91D ASP* 1.3 65.2 + - - +
92D LYS 3.0 25.8 - - - +
93D VAL* 4.2 5.8 - - + -
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Residues in contact with ASP 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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77D ASN* 3.1 15.2 + - - +
78D ASP* 2.9 33.4 + - - +
90D VAL* 1.3 78.7 - - - +
92D LYS* 1.3 61.3 + - + +
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Residues in contact with LYS 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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332C GLU* 6.5 0.9 - - + -
333C ASN* 2.7 36.3 + - - +
75D VAL* 4.5 16.6 - - + -
76D LEU 3.3 9.0 - - - +
77D ASN* 3.8 11.7 - - - +
90D VAL* 3.0 8.2 - - - +
91D ASP* 1.3 86.6 - - + +
93D VAL* 1.3 65.2 + - - +
94D LYS* 6.2 1.3 - - + -
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Residues in contact with VAL 93 (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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333C ASN* 3.6 17.7 - - + +
335C VAL* 4.0 19.5 - - + -
360C LEU* 4.3 4.7 - - + -
75D VAL* 3.3 3.4 - - - -
76D LEU* 2.9 43.6 + - + +
79D VAL* 3.4 28.9 - - + -
81D PHE* 3.8 27.8 - - + -
90D VAL* 4.2 5.2 - - + -
92D LYS* 1.3 79.8 - - - +
94D LYS* 1.3 66.8 + - - +
95D ILE* 4.1 5.2 + - + -
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Residues in contact with LYS 94 (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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332C GLU* 3.7 22.8 + - + +
333C ASN 3.1 13.0 + - - +
334C VAL* 3.3 11.6 - - + +
335C VAL 2.9 25.6 + - - +
73D THR* 4.2 22.3 - - + +
74D PHE 3.4 12.1 - - - +
75D VAL* 4.3 14.7 - - + +
92D LYS* 5.3 1.8 - - + +
93D VAL* 1.3 72.5 - - - +
95D ILE* 1.3 63.2 + - - +
96D VAL* 4.3 15.0 - - + -
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Residues in contact with ILE 95 (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* 3.4 35.0 - - + +
337C CYS* 4.2 15.3 - - - -
351C PHE* 5.8 0.7 - - + -
353C LEU* 4.2 11.4 - - + -
58D PHE* 3.8 34.5 - - + -
72D TRP 3.5 1.7 - - - +
73D THR* 3.2 4.9 - - - -
74D PHE* 2.8 55.8 + - + -
76D LEU* 4.2 17.9 - - + -
81D PHE* 5.2 2.5 - - + -
93D VAL* 4.4 9.4 - - + +
94D LYS* 1.3 78.8 - - - +
96D VAL* 1.3 65.9 + - - +
97D ALA* 4.7 2.5 - - + -
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Residues in contact with VAL 96 (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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334C VAL* 5.3 2.9 - - + -
335C VAL 2.9 11.0 + - - +
336C VAL* 3.5 12.1 - - + -
337C CYS* 3.0 25.7 + - - +
5D LEU* 4.4 12.1 - - + +
71D VAL* 4.0 21.3 - - + -
72D TRP 3.4 3.6 - - - +
73D THR* 4.4 11.2 - - + +
94D LYS* 4.3 26.2 - - + +
95D ILE* 1.3 75.8 - - - +
97D ALA* 1.3 64.1 + - - +
98D CYS* 4.4 0.7 - - - -
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Residues in contact with ALA 97 (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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337C CYS* 3.1 23.1 - - - +
339C TYR* 3.3 30.9 - - + +
353C LEU* 4.4 5.6 - - + -
71D VAL* 3.5 4.3 - - - -
72D TRP* 2.7 45.3 + - + +
74D PHE* 5.3 1.6 - - + -
95D ILE* 4.7 4.9 - - + -
96D VAL* 1.3 77.4 - - - +
98D CYS* 1.3 62.9 + - - +
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Residues in contact with CYS 98 (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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337C CYS 3.0 7.9 + - - +
338C GLN* 2.8 9.5 - - + -
339C TYR* 2.7 30.5 + - - -
3D TYR* 3.7 33.2 - - + -
5D LEU* 3.4 30.9 - - + +
70D ASN 4.4 4.0 - - - -
71D VAL* 3.9 23.6 - - + -
96D VAL* 5.6 0.4 - - - -
97D ALA* 1.3 73.4 - - - +
99D ASP* 1.3 56.8 + - - +
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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