Contacts of the helix formed by residues 86 - 104 (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 ASN 86 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q VAL* 5.8 0.9 - - + -
83Q ALA* 3.0 13.8 + - + +
85Q ASN* 1.3 86.2 + - - +
87Q THR* 1.3 61.2 + - - +
88Q LYS* 3.3 11.8 + - - +
89Q SER* 2.7 65.7 + - - +
90Q PHE 3.4 3.5 + - - -
124Q THR* 3.3 2.5 + - - -
125Q VAL* 4.2 2.4 - - - +
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Residues in contact with THR 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Q ASN* 1.3 72.4 - - - +
88Q LYS* 1.3 62.2 + - - +
90Q PHE* 3.1 6.7 + - + +
91Q GLU* 2.9 52.9 + - + +
124Q THR* 3.2 31.1 + - - -
125Q VAL* 4.0 11.6 - - + +
129Q GLN* 6.1 1.3 - - - +
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Residues in contact with LYS 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q GLN* 5.2 8.0 + - - +
86Q ASN* 3.2 10.0 - - - +
87Q THR* 1.3 78.2 - - - +
89Q SER* 1.3 58.8 + - - +
91Q GLU* 3.2 18.6 + - + +
92Q ASP* 2.7 60.9 + - - +
95Q GLN* 4.8 4.0 + - - +
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Residues in contact with SER 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q ALA* 3.9 10.0 + - - +
14Q VAL* 3.5 27.6 - - - -
81Q VAL 4.9 1.0 - - - +
82Q PHE* 3.6 10.6 - - - +
83Q ALA 3.1 21.1 + - - -
86Q ASN* 2.7 39.6 + - - +
88Q LYS* 1.3 73.1 - - - +
90Q PHE* 1.3 62.6 + - - +
92Q ASP* 3.3 20.2 + - - +
93Q ILE* 3.5 10.0 + - - +
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Residues in contact with PHE 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Q PHE* 3.7 36.3 - + + -
86Q ASN 3.4 0.6 + - - -
87Q THR* 3.1 12.2 + - + +
89Q SER* 1.3 81.9 + - - +
91Q GLU* 1.3 68.9 - - + +
93Q ILE* 3.1 22.2 + - + +
94Q HIS 4.6 0.5 + - - -
113Q LEU* 4.6 1.1 - - + -
125Q VAL* 3.8 27.4 - - + -
129Q GLN* 3.5 39.3 - - + -
130Q ALA* 3.6 36.8 - - + -
133Q LEU* 3.8 29.1 - - + +
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Residues in contact with GLU 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87Q THR* 2.9 41.6 + - + +
88Q LYS* 3.2 22.2 + - + +
90Q PHE* 1.3 85.3 - - + +
92Q ASP* 1.3 57.0 + - - +
94Q HIS* 2.8 34.2 + - - -
95Q GLN* 3.9 1.7 + - - -
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Residues in contact with ASP 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q ALA* 3.5 22.2 - - + +
61Q GLN* 4.5 8.5 - - - +
88Q LYS* 2.7 54.0 + - - +
89Q SER* 3.6 8.9 - - - +
90Q PHE 3.1 0.6 - - - -
91Q GLU* 1.3 76.0 - - - +
93Q ILE* 1.3 66.1 + - - +
94Q HIS 3.3 0.7 - - - -
95Q GLN* 3.0 39.9 + - - +
96Q TYR* 3.3 24.1 - - + -
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Residues in contact with ILE 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Q GLY* 5.4 0.7 - - - -
80Q CYS* 4.0 19.1 - - + +
81Q VAL 3.7 31.2 - - - +
82Q PHE* 4.0 17.0 - - + -
89Q SER 3.5 8.2 + - - +
90Q PHE* 3.1 18.3 + - + +
92Q ASP* 1.3 76.8 - - - +
94Q HIS* 1.3 66.0 + - - +
96Q TYR* 2.9 23.6 + - + +
97Q ARG* 3.0 12.0 + - + +
113Q LEU* 3.9 21.5 - - + -
133Q LEU* 3.9 21.5 - - + -
137Q TYR* 4.1 12.1 - - + -
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Residues in contact with HIS 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90Q PHE 4.6 0.4 + - - -
91Q GLU 2.8 30.2 + - - -
93Q ILE* 1.3 79.1 - - - +
95Q GLN* 1.3 80.9 + - + +
97Q ARG* 3.7 1.1 - - - +
98Q GLU* 2.7 66.1 + - - +
133Q LEU* 5.2 4.2 - - + +
137Q TYR* 3.2 24.0 + - - +
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Residues in contact with GLN 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Q LYS* 4.8 3.7 + - - +
91Q GLU 3.9 5.5 + - - -
92Q ASP* 3.0 40.8 + - - +
94Q HIS* 1.3 100.7 - - + +
96Q TYR* 1.3 60.6 + - + +
98Q GLU* 3.7 8.2 - - - +
99Q GLN* 2.9 30.1 + - - +
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Residues in contact with TYR 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q VAL* 4.0 30.5 - - + -
10Q GLY* 3.3 38.0 + - - -
11Q ALA* 3.7 4.5 + - - -
58Q THR* 6.1 0.4 - - - -
60Q GLY* 4.0 0.4 - - - -
61Q GLN* 3.1 32.1 + - + +
68Q ARG* 3.5 30.5 + - - -
72Q MET* 4.6 3.4 - - + -
80Q CYS* 4.9 7.0 - - + -
92Q ASP* 3.3 35.8 + - + -
93Q ILE* 2.9 13.3 + - + +
95Q GLN* 1.3 79.2 - - + +
97Q ARG* 1.3 58.9 + - - +
99Q GLN* 3.2 15.4 + - - +
100Q ILE* 2.9 36.7 + - + +
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Residues in contact with ARG 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Q CYS* 5.3 2.3 - - - -
93Q ILE* 3.0 12.9 + - + +
94Q HIS 3.7 6.5 - - - +
96Q TYR* 1.3 75.8 - - - +
98Q GLU* 1.3 65.0 + - - +
100Q ILE* 3.3 10.3 + - - +
101Q LYS* 2.9 55.6 + - - +
107Q ASP* 3.3 33.7 + - - -
111Q MET* 4.1 21.6 - - + +
136Q SER 4.9 2.2 + - - -
137Q TYR* 3.6 72.5 + - + +
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Residues in contact with GLU 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Q HIS* 2.7 55.1 + - - +
95Q GLN* 3.7 7.7 - - - +
97Q ARG* 1.3 85.1 - - - +
99Q GLN* 1.3 56.5 + - - +
101Q LYS* 3.3 9.9 + - + +
102Q ARG* 2.8 31.0 + - - +
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Residues in contact with GLN 99 (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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65Q SER* 3.9 7.5 + - - +
68Q ARG* 3.5 27.8 + - - +
69Q ASP* 2.5 30.4 + - - +
72Q MET* 3.0 31.2 - - - +
95Q GLN 2.9 18.8 + - - +
96Q TYR* 3.5 12.3 - - - +
98Q GLU* 1.3 75.6 - - - +
100Q ILE* 1.3 52.1 + - - +
102Q ARG* 3.1 24.9 + - - +
103Q VAL* 2.7 40.3 + - + +
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Residues in contact with ILE 100 (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* 4.5 7.6 - - + -
72Q MET* 3.8 23.3 - - + -
78Q PHE* 3.6 51.6 - - + -
80Q CYS* 4.1 13.5 - - - -
96Q TYR 2.9 22.8 + - - +
97Q ARG 3.6 3.6 - - - +
99Q GLN* 1.3 74.8 - - - +
101Q LYS* 1.3 64.2 + - - +
103Q VAL* 4.7 1.8 - - - -
104Q LYS* 3.0 27.7 + - + +
109Q VAL* 4.1 13.0 - - + -
111Q MET* 3.7 30.3 - - + -
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Residues in contact with LYS 101 (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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97Q ARG* 2.9 40.9 + - - +
98Q GLU* 3.6 9.4 - - + +
100Q ILE* 1.3 78.1 - - - +
102Q ARG* 1.3 58.7 + - - +
105Q ASP* 2.8 29.1 + - - -
106Q SER 3.1 27.4 + - - +
107Q ASP* 3.3 36.3 + - - +
109Q VAL* 5.1 1.1 - - - -
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Residues in contact with ARG 102 (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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69Q ASP* 2.8 38.0 + - - -
98Q GLU 2.8 17.9 + - - +
99Q GLN* 3.3 22.5 - - - +
101Q LYS* 1.3 73.8 - - - +
103Q VAL* 1.3 75.3 + - - +
105Q ASP* 2.8 18.6 + - - +
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Residues in contact with VAL 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Q ASP* 3.4 39.9 - - + +
72Q MET* 4.0 12.6 - - + -
73Q ARG* 3.8 52.7 + - + +
99Q GLN* 2.7 28.4 + - + +
100Q ILE 4.1 2.0 - - - +
102Q ARG* 1.3 81.0 - - - +
104Q LYS* 1.3 60.6 + - - +
105Q ASP* 3.4 2.1 + - - +
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Residues in contact with LYS 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72Q MET* 3.3 12.6 + - + +
73Q ARG* 3.0 25.0 + - - +
74Q THR 4.5 0.6 - - - -
75Q GLY 2.9 24.5 + - - -
76Q GLU* 5.2 2.5 - - - +
78Q PHE* 3.7 26.9 - - + -
100Q ILE* 3.0 16.0 + - + +
103Q VAL* 1.3 77.4 - - + +
105Q ASP* 1.3 73.0 + - - +
106Q SER* 3.3 5.1 + - - -
109Q VAL* 3.9 26.0 - - + -
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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
------------------------------------------------------------
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