Contacts of the helix formed by residues 84 - 101 (chain F) in PDB entry 1NZB
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 ALA 84 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82F GLY 3.8 0.2 + - - -
83F LEU* 1.3 75.9 - - - +
85F VAL* 1.3 68.4 + - - +
86F LYS 4.3 2.2 - - - +
87F THR* 2.9 15.9 + - - +
88F ILE* 3.1 11.3 + - - +
129F GLU* 3.4 13.2 - - + +
113G T 2.8 50.6 + - - +
114G A 4.6 3.6 - - - +
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Residues in contact with VAL 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E LEU* 3.9 30.1 - - + -
83F LEU 3.8 0.4 + - - -
84F ALA* 1.3 73.4 - - - +
86F LYS* 1.3 65.0 + - - +
88F ILE* 3.0 11.9 + - - +
89F GLN* 3.0 29.6 + - + +
117F MET* 4.5 3.9 - - + +
120F ILE* 4.5 1.8 - - + +
121F ARG* 3.6 37.0 - - + +
124F ASN* 3.6 29.6 - - + +
129F GLU* 2.6 26.0 + - + +
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Residues in contact with LYS 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E LEU* 4.9 8.4 - - + +
204E VAL* 4.0 24.5 - - - +
84F ALA* 3.2 1.0 - - - +
85F VAL* 1.3 81.2 - - - +
87F THR* 1.3 62.6 + - - +
89F GLN* 3.2 26.4 + - + +
90F GLN* 3.1 21.7 + - - +
131F ALA* 5.4 5.6 - - + -
113G T 4.1 7.7 - - + -
114G A 3.4 53.0 + - + +
115G A 3.4 36.2 + - - +
116G T 5.3 7.2 + - - +
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Residues in contact with THR 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F LEU* 4.2 14.8 - - + -
84F ALA* 2.9 10.0 + - - +
86F LYS* 1.3 79.2 - - - +
88F ILE* 1.3 60.8 + - - +
90F GLN* 3.5 2.6 + - - +
91F HIS* 2.8 35.0 + - + +
5309F MG 3.7 14.4 - - - -
112G A 3.1 5.1 - - + +
113G T 2.7 76.5 + - + +
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Residues in contact with ILE 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F LEU* 3.8 30.5 - - + +
78F LEU* 3.9 23.1 - - + -
79F GLN* 3.9 19.5 - - + +
83F LEU* 3.8 18.8 - - + +
84F ALA 3.1 15.7 + - - +
85F VAL* 3.0 8.0 + - - +
87F THR* 1.3 74.9 - - - +
89F GLN* 1.3 65.9 + - - +
90F GLN 3.0 3.0 + - - -
91F HIS* 3.0 12.3 + - - +
92F LEU* 3.0 11.8 + - - +
117F MET* 3.7 19.7 - - + -
120F ILE* 3.7 26.9 - - + -
124F ASN* 5.1 1.1 - - - +
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Residues in contact with GLN 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E LEU* 4.6 7.3 - - - +
85F VAL* 3.0 29.1 + - + +
86F LYS* 3.2 37.4 + - + +
88F ILE* 1.3 76.5 - - - +
90F GLN* 1.3 52.1 + - - +
92F LEU* 3.8 3.4 - - - +
93F GLY* 2.7 27.9 + - - -
117F MET* 4.0 26.5 - - + +
121F ARG* 4.0 12.3 - - - +
5307F MG 4.0 7.1 - - - -
119H A 3.4 24.0 + - - -
122H T 5.6 0.2 - - - +
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Residues in contact with GLN 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F MET* 3.2 43.2 - - + +
48F VAL* 4.4 3.4 - - + -
86F LYS 3.1 10.5 + - - +
87F THR 3.7 8.7 - - - +
88F ILE 3.0 1.0 - - - -
89F GLN* 1.3 74.9 - - - +
91F HIS* 1.3 67.1 + - - +
92F LEU 3.1 1.8 - - - -
93F GLY* 2.7 2.8 + - - +
94F GLN* 2.7 39.4 + - + +
113G T 3.6 18.6 - - + +
114G A 3.0 18.0 - - - +
122H T 3.7 14.0 + - - +
123H T 2.9 26.5 + - - +
124H A 3.9 0.2 + - - -
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Residues in contact with HIS 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F SER* 5.4 2.2 - - - -
48F VAL* 3.4 34.4 - - + +
51F SER* 4.2 10.5 - - - -
74F TYR* 3.3 28.5 + - + -
75F LEU* 4.9 1.3 - - + -
78F LEU* 3.5 31.8 - - + +
81F ARG* 6.2 0.2 - - - -
83F LEU* 5.0 1.8 - - - +
87F THR* 2.8 31.9 + - + +
88F ILE 3.0 3.6 + - - +
90F GLN* 1.3 79.3 - - + +
92F LEU* 1.3 63.3 + - - +
95F LEU* 2.8 31.4 + - - +
5309F MG 2.3 31.3 - - - -
112G A 4.4 4.2 + - - -
113G T 4.7 3.3 - - + +
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Residues in contact with LEU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F VAL* 4.2 9.6 - - + -
75F LEU* 3.9 24.5 - - + +
88F ILE 3.0 13.8 + - - +
89F GLN* 3.9 4.7 - - - +
91F HIS* 1.3 76.9 - - - +
93F GLY* 1.3 64.3 + - - +
95F LEU* 3.3 8.0 + - + +
96F ASN* 3.0 36.8 + - - +
107F PRO* 4.6 2.7 - - + -
108F SER* 3.4 24.7 - - - +
113F VAL* 3.7 20.9 - - + -
114F SER* 6.1 0.4 - - - -
117F MET* 3.8 34.8 - - + -
120H C 5.8 1.1 - - - +
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Residues in contact with GLY 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F GLN 2.7 19.8 + - - -
90F GLN* 2.7 8.3 + - - -
92F LEU* 1.3 78.8 - - - +
94F GLN* 1.3 59.7 + - - -
96F ASN* 3.4 10.7 + - - +
97F MET* 3.3 16.8 + - - +
5307F MG 4.4 7.4 - - - -
121H A 5.8 3.6 - - - +
122H T 4.1 19.5 - - - +
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Residues in contact with GLN 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F THR* 4.2 5.0 - - - +
44F MET* 3.8 19.6 - - - +
45F LEU* 4.0 33.4 - - + +
48F VAL* 3.9 20.6 - - + -
49F CYS* 6.2 0.7 - - - -
90F GLN* 2.7 40.4 + - - +
93F GLY* 1.3 68.6 - - - -
95F LEU* 1.3 67.8 + - - +
97F MET* 2.8 39.4 + - - +
98F LEU* 3.0 14.9 + - - +
122H T 4.2 7.1 - - - +
123H T 3.7 19.1 - - - +
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F VAL* 3.2 23.3 - - + -
49F CYS* 5.8 5.2 - - - -
52F TRP* 3.8 46.0 - - + +
63F TRP* 5.2 0.7 - - + +
66F ALA* 4.7 4.5 - - + -
71F VAL* 5.2 10.5 - - + -
74F TYR* 4.7 7.9 - - + -
91F HIS 2.8 28.4 + - - +
92F LEU* 3.5 13.2 - - + +
94F GLN* 1.3 76.5 - - - +
96F ASN* 1.3 61.3 + - - +
98F LEU* 3.6 10.0 + - + +
99F HIS* 2.7 46.7 + - + -
107F PRO* 4.4 11.2 - - + -
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Residues in contact with ASN 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F LEU* 3.0 29.2 + - - +
93F GLY* 3.6 7.0 - - - +
94F GLN 3.1 0.2 - - - -
95F LEU* 1.3 76.9 - - - +
97F MET* 1.3 58.4 + - - +
99F HIS* 3.4 0.7 + - - +
100F ARG* 2.8 26.9 + - - +
106F ARG* 3.4 26.9 - - - +
107F PRO* 2.9 29.4 - - - +
108F SER* 3.0 40.0 + - - -
5307F MG 4.3 10.5 - - - -
120H C 5.1 0.2 + - - -
121H A 4.9 5.5 + - - +
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Residues in contact with MET 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F MET* 4.2 20.4 - - + -
37F PHE* 4.5 15.3 - - + -
41F THR* 4.3 13.2 - - + -
42F TRP* 5.1 0.2 - - - +
45F LEU* 3.8 29.8 - - + -
93F GLY 3.3 9.1 + - - +
94F GLN* 2.8 27.1 + - - +
96F ASN* 1.3 75.3 - - - +
98F LEU* 1.3 66.8 + - - +
99F HIS 2.9 2.1 + - - -
100F ARG* 3.1 4.3 + - - +
101F ARG* 2.8 35.1 + - - +
121H A 5.6 5.4 - - + -
122H T 3.5 47.8 - - + +
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Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F LEU* 4.3 9.5 - - + +
30F MET* 4.3 21.3 - - + -
31F PHE* 4.6 12.3 - - + -
45F LEU* 4.3 19.9 - - + +
49F CYS* 3.8 25.1 - - - -
63F TRP* 4.4 11.7 - - + -
64F PHE* 4.0 28.7 - - + -
94F GLN 3.0 11.1 + - - +
95F LEU* 3.8 11.2 - - + +
97F MET* 1.3 81.6 - - - +
99F HIS* 1.3 62.6 + - + +
101F ARG* 4.1 4.5 - - - +
102F SER* 2.9 26.0 + - - -
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Residues in contact with HIS 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F TRP 5.3 0.4 - - - -
64F PHE* 3.7 25.8 - + - -
65F PRO* 3.8 12.6 - - + +
66F ALA* 3.0 43.2 + - + +
95F LEU* 2.7 33.5 + - + +
96F ASN 3.6 6.7 - - - +
97F MET 2.9 1.6 + - - -
98F LEU* 1.3 78.3 - - + +
100F ARG* 1.3 58.5 + - - +
102F SER* 2.6 33.9 + - - -
103F GLY 3.1 4.0 + - - -
104F LEU* 3.5 12.7 + - + +
105F PRO 3.7 24.7 - - - +
106F ARG* 4.2 5.2 - - - -
107F PRO* 4.0 11.7 - - + -
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Residues in contact with ARG 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F ASN 2.8 20.7 + - - +
97F MET* 3.9 3.8 - - - +
99F HIS* 1.3 73.2 - - - +
101F ARG* 1.3 93.0 + - - +
102F SER 2.8 5.9 + - - -
103F GLY* 3.0 13.2 + - - -
104F LEU 3.9 9.4 + - - +
106F ARG* 4.0 20.1 - - + +
121H A 3.3 42.5 + - - -
122H T 3.5 9.9 + - - -
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Residues in contact with ARG 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASN* 5.0 11.2 + - - +
115A LEU* 4.5 17.1 - - + +
118A ARG* 4.0 17.0 - - - +
26F ASN* 3.9 17.7 - - - +
27F LEU* 4.4 2.7 - - + +
30F MET* 3.3 36.7 - - + +
37F PHE* 4.0 16.4 - - - -
97F MET* 2.8 26.4 + - - +
98F LEU 4.1 3.1 - - - +
100F ARG* 1.3 93.1 - - - +
102F SER* 1.3 60.7 + - - +
122H T 2.5 52.7 + - - -
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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