Contacts of the helix formed by residues 98 - 111 (chain G) in PDB entry 1NZX
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 ASP 98 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94G LEU 3.1 9.5 + - - +
95G ILE 3.3 6.1 - - - +
97G ARG* 1.3 116.3 + - - +
99G ARG* 1.3 57.4 + - - +
100G THR 3.5 2.2 - - - -
101G TYR* 3.4 11.7 + - + -
102G LEU* 2.9 33.8 + - + +
203G TYR* 2.6 42.5 + - + +
207G LEU* 3.5 5.7 - - + +
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Residues in contact with ARG 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G ILE 3.0 9.9 + - - +
96G GLU* 3.1 35.3 + - - +
97G ARG 3.2 1.8 + - - -
98G ASP* 1.3 76.1 - - - +
100G THR* 1.3 57.1 - - - +
102G LEU* 3.2 1.9 + - - +
103G ALA* 2.8 32.9 + - - +
118G TYR* 2.8 67.5 + - + +
119G LEU* 4.1 8.5 - - - +
122G LEU* 3.8 25.3 - - + +
123G ASP* 3.7 28.4 + - - +
126G LEU* 4.8 12.4 - - + +
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Residues in contact with THR 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G PRO* 3.8 15.6 - - + +
10G ALA 4.0 16.8 - - - +
11G PRO* 4.8 4.5 - - + -
12G ASN 5.4 1.8 - - - +
97G ARG 5.1 1.0 + - - -
98G ASP 3.5 0.2 - - - -
99G ARG* 1.3 76.9 - - - +
101G TYR* 1.3 65.0 + - - +
103G ALA* 3.5 2.1 + - - +
104G ALA* 3.1 22.9 + - - +
114G TYR* 3.5 19.7 - - + +
118G TYR* 3.6 22.0 + - - -
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Residues in contact with TYR 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ASN* 5.7 4.5 - - + -
15G PRO* 4.1 20.0 - - + -
16G GLU 2.7 32.0 + - - -
17G VAL* 4.2 0.5 - - - -
18G PHE* 3.2 29.3 + + - -
98G ASP* 3.4 14.0 + - + +
99G ARG 3.3 0.6 - - - -
100G THR* 1.3 78.9 - - - +
102G LEU* 1.3 61.8 + - + +
104G ALA* 3.2 6.6 + - - +
105G LEU* 2.9 50.5 + - + +
203G TYR* 3.7 47.5 - + - -
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Residues in contact with LEU 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G ILE* 4.0 36.3 - - + +
98G ASP* 2.9 23.0 + - + +
99G ARG 3.8 2.9 - - - +
101G TYR* 1.3 78.2 - - + +
103G ALA* 1.3 61.3 + - - +
105G LEU* 3.3 1.9 + - + -
106G GLU* 2.8 31.2 + - - +
122G LEU* 4.1 13.2 - - + -
172G LEU* 4.2 7.1 - - + +
200G THR* 3.8 35.7 - - + +
203G TYR* 3.7 28.0 - - + -
204G VAL* 4.3 8.5 - - + -
207G LEU* 4.3 14.1 - - + -
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Residues in contact with ALA 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G ARG 2.8 20.2 + - - +
100G THR 3.8 0.2 - - - +
102G LEU* 1.3 72.9 - - - +
104G ALA* 1.3 57.7 + - - +
106G GLU* 3.4 3.0 + - - +
107G THR* 3.0 26.0 + - - -
114G TYR* 3.8 17.0 - - + -
117G SER* 3.4 12.3 - - - -
118G TYR* 3.7 37.2 - - + +
122G LEU* 3.7 12.4 - - + +
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Residues in contact with ALA 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ASN* 3.6 31.0 - - + +
15G PRO* 4.2 8.3 - - + -
100G THR* 3.1 14.1 + - + +
101G TYR* 3.5 10.3 - - - +
102G LEU 3.2 0.2 - - - -
103G ALA* 1.3 74.7 - - - +
105G LEU* 1.3 60.3 + - - +
107G THR 3.3 1.4 + - - -
108G LEU* 2.9 28.4 + - - +
114G TYR* 3.9 15.2 - - + -
335G PHE* 3.5 14.2 - - + -
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Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G PRO* 4.0 23.3 - - + +
16G GLU 5.1 0.2 - - - +
17G VAL* 4.5 13.2 - - + -
101G TYR* 2.9 44.9 + - + +
102G LEU* 3.8 5.8 - - + +
104G ALA* 1.3 73.1 - - - +
106G GLU* 1.3 65.9 + - - +
108G LEU* 3.6 7.6 - - + +
109G ASP* 3.1 23.0 + - - +
199G LEU* 3.8 33.7 - - + +
200G THR* 3.7 30.4 - - + +
203G TYR* 4.6 6.1 - - + -
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Residues in contact with GLU 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G LEU 2.8 18.4 + - - +
103G ALA* 3.4 9.6 - - - +
104G ALA 3.2 0.2 - - - -
105G LEU* 1.3 77.6 - - - +
107G THR* 1.3 53.0 + - - +
109G ASP* 3.9 2.4 - - - +
110G ASN* 2.8 39.1 + - + +
112G LYS* 4.4 12.8 - - + -
117G SER* 3.9 14.4 - - - +
121G ASP* 4.5 10.7 - - + +
122G LEU* 5.1 0.4 - - + -
170G PHE 4.4 0.7 - - - -
171G PRO* 3.2 24.5 - - - +
172G LEU* 2.9 41.0 + - + +
197G THR* 5.6 0.3 - - - -
200G THR* 2.7 27.3 + - + +
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Residues in contact with THR 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G ASN* 5.1 0.2 - - - +
43G SER* 5.1 0.9 + - - -
103G ALA 3.0 8.1 + - - -
104G ALA 3.3 3.8 + - - -
106G GLU* 1.3 78.7 - - - +
108G LEU* 1.3 59.6 + - - +
111G GLY* 2.8 28.4 + - - +
112G LYS* 2.6 29.8 + - - +
114G TYR* 3.1 19.8 - - - +
117G SER* 2.9 17.6 + - - -
334G PRO* 3.6 24.0 - - + +
335G PHE* 3.8 24.2 - - + -
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Residues in contact with LEU 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G GLN 3.7 23.6 - - - +
14G GLN* 5.0 2.5 - - - -
15G PRO* 3.7 29.2 - - + +
41G ASN* 3.3 51.5 - - - +
42G PRO* 3.6 5.0 - - - +
48G ILE* 3.6 29.1 - - + +
104G ALA 2.9 17.4 + - - +
105G LEU* 3.6 13.2 - - + +
106G GLU 3.3 0.2 - - - -
107G THR* 1.3 80.5 - - - +
109G ASP* 1.3 60.0 + - - +
335G PHE* 4.0 11.7 - - + -
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Residues in contact with ASP 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G THR* 2.7 12.9 + - - -
40G VAL 3.6 1.7 - - - +
42G PRO* 3.5 7.6 - - - +
48G ILE* 3.7 5.7 - - - +
105G LEU 3.1 14.0 + - - +
106G GLU* 4.1 2.9 - - - +
108G LEU* 1.3 80.5 - - - +
110G ASN* 1.3 57.2 + - - +
196G GLN 3.6 8.0 - - - +
197G THR* 3.3 24.6 - - + +
198G PRO* 3.3 5.5 - - - +
199G LEU* 3.3 37.8 + - + +
200G THR* 5.0 2.2 + - + +
345G VAL* 4.8 2.4 - - - +
1707G NA 2.3 51.4 - - - -
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Residues in contact with ASN 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G PRO* 3.4 11.6 - - - +
106G GLU 2.8 23.5 + - - +
109G ASP* 1.3 75.9 - - - +
111G GLY* 1.3 54.7 + - - +
112G LYS* 2.9 47.3 + - - +
168G TRP* 2.9 31.9 + - - -
169G ASN* 3.4 17.8 + - - +
171G PRO* 3.9 9.3 - - + +
197G THR* 4.0 11.8 - - + +
297G ASN* 4.3 2.0 + - - +
298G GLN* 4.3 3.5 + - - -
300G GLN* 5.0 5.9 + - - +
343G PRO 4.4 3.1 - - - +
345G VAL* 4.0 16.1 + - - +
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Residues in contact with GLY 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G PRO* 3.7 14.3 - - - +
43G SER* 4.4 3.8 - - - -
107G THR 2.8 21.4 + - - -
110G ASN* 1.3 75.2 - - - +
112G LYS* 1.3 66.2 + - - +
298G GLN* 4.4 4.0 - - - -
334G PRO* 3.3 9.6 - - - +
342G GLY* 3.5 4.5 - - - -
343G PRO* 3.2 30.2 - - - +
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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