Contacts of the strand formed by residues 77 - 83 (chain Q) in PDB entry 1NVU
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 77 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5Q LYS 3.3 4.5 + - - +
6Q LEU* 3.5 2.8 - - - -
7Q VAL* 2.9 26.5 + - - +
75Q GLY 3.6 0.2 - - - -
76Q GLU* 1.3 82.6 - - - +
78Q PHE* 1.3 67.1 + - - -
110Q PRO 3.2 10.8 - - - -
159Q LEU* 3.9 10.3 - - - +
163Q ILE* 3.7 16.1 - - - +
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Residues in contact with PHE 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q VAL* 3.2 30.1 - - + +
9Q VAL* 4.4 5.2 - - + -
72Q MET* 3.4 53.2 - - + -
75Q GLY* 4.0 15.5 - - - -
77Q GLY* 1.3 79.7 - - - -
79Q LEU* 1.3 62.3 + - - +
80Q CYS* 3.8 3.8 - - - -
100Q ILE* 3.6 33.7 - - + -
104Q LYS* 3.7 11.2 - - + -
109Q VAL* 3.6 31.6 - - + -
110Q PRO 3.0 5.4 + - - -
111Q MET* 3.0 13.1 - - + +
112Q VAL 3.0 24.3 + - - -
159Q LEU* 3.7 6.4 - - - +
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Residues in contact with LEU 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q VAL 2.8 11.3 + - - +
8Q VAL* 3.6 15.9 - - + -
9Q VAL* 2.9 29.6 + - - +
19Q LEU* 5.3 4.7 - - + -
78Q PHE* 1.3 72.5 - - - +
80Q CYS* 1.3 60.4 + - - +
81Q VAL* 3.7 4.7 + - + +
112Q VAL* 3.6 17.7 - - + -
114Q VAL* 3.7 19.5 - - + -
155Q ALA* 3.7 26.9 - - + +
156Q PHE* 3.7 44.9 - - + -
159Q LEU* 3.5 24.8 - - + +
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Residues in contact with CYS 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q VAL* 3.7 20.2 - - + -
78Q PHE* 4.4 4.3 - - - -
79Q LEU* 1.3 73.2 - - - +
81Q VAL* 1.3 60.3 + - - +
93Q ILE* 4.0 20.9 - - + -
96Q TYR* 4.9 6.1 - - + -
97Q ARG* 5.3 3.8 - - - -
100Q ILE* 4.1 12.6 - - - -
111Q MET* 3.8 29.4 - - - -
112Q VAL 2.9 12.7 + - - +
113Q LEU* 3.6 15.5 - - + +
114Q VAL 2.8 24.1 + - - +
139Q ILE* 6.0 1.1 - - + -
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Residues in contact with VAL 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q VAL* 3.9 23.1 - - + -
9Q VAL 2.9 17.9 + - - +
10Q GLY* 3.5 19.8 - - - -
11Q ALA 4.1 2.4 + - - -
14Q VAL* 3.7 25.2 - - + +
16Q LYS* 4.3 2.9 - - + +
19Q LEU* 4.0 17.0 - - + -
79Q LEU* 4.0 8.3 - - + +
80Q CYS* 1.3 76.9 - - - +
82Q PHE* 1.3 74.0 + - - +
89Q SER 4.9 0.5 - - - +
93Q ILE* 3.7 6.8 - - - +
114Q VAL* 3.4 18.2 - - + +
116Q ASN* 3.9 17.3 - - + -
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Residues in contact with PHE 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q VAL* 4.0 10.1 - - - -
81Q VAL* 1.3 74.7 - - - +
83Q ALA* 1.3 65.4 + - - +
84Q ILE* 4.1 9.6 - - + -
89Q SER* 3.5 29.2 - - - +
90Q PHE* 3.7 33.0 - + + -
93Q ILE* 4.0 4.5 - - + -
113Q LEU* 3.9 22.2 - - + -
114Q VAL 3.0 25.2 + - - +
115Q GLY* 3.6 9.2 - - - -
116Q ASN* 2.7 33.8 + - - +
125Q VAL* 3.8 23.8 - - + -
130Q ALA* 3.7 7.0 - - + -
141Q TYR* 3.5 37.2 - + - -
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Residues in contact with ALA 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q VAL* 3.9 16.0 - - + +
82Q PHE* 1.3 81.1 - - - +
84Q ILE* 1.3 59.0 + - - +
85Q ASN* 2.9 26.8 + - - +
86Q ASN* 3.0 29.3 + - + +
89Q SER* 3.1 6.4 + - - +
116Q ASN 3.5 5.8 - - - -
117Q LYS* 3.9 24.0 - - + +
125Q VAL* 4.3 0.3 - - - +
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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