Contacts of the helix formed by residues 100 - 113 (chain D) in PDB entry 1NZ0
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 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D TRP* 3.8 8.3 - - - -
98D ARG 4.4 0.4 + - - -
99D VAL* 1.3 78.8 - - - +
101D PHE* 1.3 67.9 + - - +
102D TRP* 3.3 22.6 + - + +
103D THR* 3.0 38.4 + - - -
104D VAL* 3.1 18.7 + - - +
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Residues in contact with PHE 101 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D TRP* 3.6 62.5 - + + -
69D GLU* 4.1 21.3 - - + -
70D ILE* 3.6 31.9 - - + -
100D ASP* 1.3 75.9 - - - +
102D TRP* 1.3 88.7 + + + +
104D VAL* 3.1 3.1 + - - +
105D ARG* 2.8 47.3 + - + +
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Residues in contact with TRP 102 (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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100D ASP* 3.2 23.1 + - + +
101D PHE* 1.3 105.1 - + + +
103D THR* 1.3 58.3 + - - +
105D ARG* 3.5 19.8 + - - +
106D GLU* 2.9 28.8 + - - +
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Residues in contact with THR 103 (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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31D TYR* 4.3 16.6 - - + +
99D VAL* 3.8 20.4 - - + -
100D ASP* 3.0 22.6 + - - -
102D TRP* 1.3 75.4 - - - +
104D VAL* 1.3 64.0 + - - +
106D GLU* 3.3 10.7 + - - +
107D LYS* 3.0 41.1 + - + +
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Residues in contact with VAL 104 (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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31D TYR* 5.8 1.3 - - + -
32D PHE* 3.8 26.7 - - + -
63D LEU* 4.4 7.9 - - + -
66D TRP* 4.1 27.8 - - + -
67D VAL* 4.8 2.2 - - + -
70D ILE* 4.0 15.7 - - + -
92D LEU* 4.4 17.0 - - + -
96D PHE* 4.7 5.4 - - + -
99D VAL* 3.6 23.8 - - + -
100D ASP 3.1 7.5 + - - +
101D PHE 3.7 6.3 - - - +
103D THR* 1.3 75.0 - - - +
105D ARG* 1.3 63.1 + - - +
107D LYS* 4.8 1.3 - - - -
108D LEU* 2.9 23.9 + - - +
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Residues in contact with ARG 105 (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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70D ILE* 3.5 28.4 - - + +
74D ASN* 4.3 15.9 + - - +
101D PHE* 2.8 38.9 + - + +
102D TRP* 3.7 19.5 + - - +
104D VAL* 1.3 74.3 - - - +
106D GLU* 1.3 74.1 + - - +
109D LEU* 2.9 56.8 + - + +
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Residues in contact with GLU 106 (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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102D TRP 2.9 18.4 + - - +
103D THR* 3.7 12.5 + - - +
105D ARG* 1.3 87.2 - - - +
107D LYS* 1.3 74.5 + - - +
109D LEU* 4.2 2.5 - - - +
110D ASN* 3.0 52.2 + - - +
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Residues in contact with LYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ASN* 2.8 36.5 + - + +
30D GLU* 2.7 31.0 + - - +
31D TYR* 3.8 28.5 - - + -
32D PHE* 4.4 9.4 - - + -
103D THR* 3.0 24.2 + - + +
104D VAL 4.0 2.0 - - - +
106D GLU* 1.3 90.8 + - - +
108D LEU* 1.3 63.4 - - - +
110D ASN* 3.7 19.2 - - - +
111D LEU* 3.7 3.6 + - - +
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D PHE* 4.0 17.2 - - + -
34D VAL* 4.1 12.6 - - + -
67D VAL* 3.9 39.0 - - + +
70D ILE* 4.1 22.9 - - + -
71D PHE* 5.4 0.7 - - + +
86D VAL* 4.0 25.6 - - + -
104D VAL 2.9 19.1 + - - +
105D ARG 4.0 2.0 - - - +
107D LYS* 1.3 78.2 - - - +
109D LEU* 1.3 63.6 + - - +
111D LEU* 3.0 5.5 + - - +
112D LEU* 3.0 47.7 + - + +
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Residues in contact with LEU 109 (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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70D ILE* 3.8 21.1 - - + -
74D ASN* 4.0 30.3 - - + +
77D VAL* 5.2 1.8 - - + -
78D ILE* 4.2 19.5 - - + -
105D ARG* 2.9 60.7 + - + +
106D GLU* 4.2 2.7 - - - +
108D LEU* 1.3 70.5 - - - +
110D ASN* 1.3 66.3 + - - +
112D LEU* 4.2 5.8 - - + +
113D LYS* 2.9 47.3 + - + +
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Residues in contact with ASN 110 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ASN* 4.6 6.0 - - - +
106D GLU* 3.0 44.2 + - - +
107D LYS* 3.7 21.0 - - - +
108D LEU 3.2 0.2 - - - -
109D LEU* 1.3 77.5 - - - +
111D LEU* 1.3 61.5 + - + +
113D LYS* 4.4 4.7 - - - +
114D ARG* 3.1 35.1 + - - +
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Residues in contact with LEU 111 (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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27D LEU* 3.5 21.7 - - + +
28D GLN* 3.8 30.5 - - - +
29D ASN* 3.4 28.9 - - + +
32D PHE* 3.6 31.0 - - + +
34D VAL* 3.8 29.4 - - + -
107D LYS 3.8 2.5 - - - +
108D LEU* 3.0 7.4 + - + +
110D ASN* 1.3 77.3 - - + +
112D LEU* 1.3 67.3 + - - +
113D LYS 3.2 2.0 - - - -
114D ARG* 3.0 28.2 + - - +
115D ILE* 3.7 1.1 + - - +
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Residues in contact with LEU 112 (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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34D VAL* 3.9 11.7 - - + -
70D ILE* 5.0 2.2 - - + -
71D PHE* 4.5 11.9 - - + -
78D ILE* 4.0 36.3 - - + -
79D PRO* 3.2 17.7 - - - +
84D ILE* 3.9 31.4 - - + -
86D VAL* 4.6 3.8 - - + -
108D LEU* 3.0 50.8 + - + +
109D LEU* 4.1 11.2 - - + +
111D LEU* 1.3 74.6 - - - +
113D LYS* 1.3 62.5 - - - +
114D ARG 3.1 0.2 - - - -
115D ILE* 3.2 26.5 + - + +
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Residues in contact with LYS 113 (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 VAL* 3.6 49.8 - - + +
78D ILE* 5.2 0.9 - - - -
79D PRO* 4.2 12.8 - - - +
109D LEU* 2.9 40.9 + - + +
110D ASN* 4.4 4.3 - - - +
111D LEU 3.2 0.2 - - - -
112D LEU* 1.3 78.6 - - + +
114D ARG* 1.3 60.8 + - + +
115D ILE 3.3 1.5 + - - +
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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