Contacts of the helix formed by residues 74 - 94 (chain A) in PDB entry 3N4H
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 THR 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLY 3.7 2.7 + - - +
73A ARG* 1.3 77.2 - - - +
75A GLU* 1.3 63.3 + - - +
76A LYS* 3.6 14.8 + - - +
77A GLN* 2.7 45.4 + - - +
78A LYS* 3.1 21.6 + - - +
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG 5.4 0.7 - - - +
74A THR* 1.3 72.9 - - - +
76A LYS* 1.3 52.2 + - - +
78A LYS* 3.7 22.1 - - - +
79A GLU* 2.8 36.7 + - - +
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 6.1 1.4 - - - -
74A THR* 3.2 11.6 + - - +
75A GLU* 1.3 76.2 - - - +
77A GLN* 1.3 79.0 + - - +
79A GLU* 3.6 9.7 - - - +
80A GLU* 2.9 65.8 + - + +
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Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.1 32.7 - - - +
32A ALA* 4.1 1.7 - - - +
33A HIS* 3.2 21.4 + - + -
72A GLY 4.7 0.6 + - - -
73A ARG* 3.4 24.5 - - + +
74A THR* 2.7 59.2 + - - +
76A LYS* 1.3 91.0 - - - +
78A LYS* 1.3 58.4 + - - +
80A GLU* 3.5 10.3 + - - +
81A LEU* 3.0 28.2 + - - +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ILE* 4.6 11.4 - - + -
73A ARG* 3.7 21.5 - - + -
74A THR 3.1 18.9 + - - +
75A GLU* 3.7 23.0 - - - +
77A GLN* 1.3 74.1 - - - +
79A GLU* 1.3 59.5 + - - +
81A LEU* 3.2 8.5 + - + +
82A LEU* 2.9 37.4 + - + +
104A ILE* 4.3 18.1 - - + +
106A GLU* 2.9 45.2 + - + +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLU* 2.8 22.7 + - - +
76A LYS* 3.6 10.6 - - - +
78A LYS* 1.3 71.0 - - - +
80A GLU* 1.3 65.5 + - + +
82A LEU* 3.4 12.1 + - + +
83A LEU* 3.1 25.1 + - + +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.8 23.5 - - + +
76A LYS* 2.9 59.1 + - + +
77A GLN* 3.8 7.7 - - - +
79A GLU* 1.3 77.7 - - + +
81A LEU* 1.3 57.4 + - - +
83A LEU* 3.4 5.0 + - - +
84A ARG* 2.8 31.2 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TYR* 3.4 22.4 - - - +
27A ALA* 3.8 34.3 - - + +
28A HIS* 4.1 12.3 - - + +
31A LEU* 3.6 12.1 - - + +
32A ALA* 4.9 8.3 - - + -
69A ILE* 4.7 11.2 - - + -
73A ARG* 6.5 0.4 - - + -
77A GLN 3.0 17.7 + - - +
78A LYS* 3.5 7.4 - - + +
79A GLU 3.2 0.2 - - - -
80A GLU* 1.3 74.9 - - - +
82A LEU* 1.3 65.0 + - - +
84A ARG* 3.4 1.0 + - - +
85A LEU* 3.0 49.5 + - + +
104A ILE* 4.1 18.4 - - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LYS* 2.9 25.9 + - + +
79A GLU* 3.8 11.7 - - + +
80A GLU 3.4 0.2 - - - -
81A LEU* 1.3 72.2 - - - +
83A LEU* 1.3 62.2 + - - +
85A LEU* 4.0 4.4 - - - +
86A THR* 2.8 32.7 + - - +
102A VAL* 3.6 40.2 - - + +
104A ILE* 3.6 28.5 - - + +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLU* 3.1 15.1 + - + +
80A GLU* 3.9 5.4 - - - +
82A LEU* 1.3 80.7 - - + +
84A ARG* 1.3 61.9 + - - +
86A THR* 3.5 5.8 + - + -
87A GLN* 3.2 44.3 + - + +
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Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASP* 3.9 5.7 - - - +
27A ALA* 3.6 35.8 - - + +
30A GLU* 2.4 44.7 + - - +
31A LEU* 3.8 26.8 - - + +
80A GLU 2.8 21.8 + - - +
81A LEU 3.8 2.9 - - - +
83A LEU* 1.3 73.4 - - - +
85A LEU* 1.3 57.5 + - - +
87A GLN* 3.3 2.8 + - - -
88A GLU* 2.8 76.4 + - + +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 3.7 26.9 - - + -
23A ALA* 4.7 1.3 - - + +
24A ILE* 3.8 34.3 - - + +
27A ALA* 3.7 25.1 - - + -
65A VAL* 5.4 1.8 - - + -
81A LEU* 3.0 34.0 + - + +
82A LEU* 4.0 3.1 - - + +
84A ARG* 1.3 74.5 - - - +
86A THR* 1.3 64.7 + - - +
88A GLU* 4.9 3.4 - - + -
89A ILE* 2.9 39.2 + - + +
102A VAL* 4.1 28.3 - - + -
104A ILE* 5.7 0.9 - - + -
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Residues in contact with THR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 2.8 23.4 + - - +
83A LEU* 3.7 8.5 - - + -
84A ARG 3.3 0.2 - - - -
85A LEU* 1.3 76.6 - - - +
87A GLN* 1.3 57.6 + - + +
90A ALA* 3.0 29.8 + - - +
97A ASN* 3.3 38.8 - - + +
100A VAL* 4.0 23.4 + - + +
102A VAL* 3.8 14.4 + - - +
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.2 34.5 + - + +
84A ARG* 4.1 3.1 - - - +
86A THR* 1.3 75.3 - - + +
88A GLU* 1.3 62.7 + - + +
90A ALA* 3.4 1.4 + - - +
91A LEU* 3.0 39.2 + - + +
97A ASN* 2.8 40.8 + - - +
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.2 38.3 - - + +
26A ASP* 5.7 0.3 - - - +
27A ALA* 5.5 0.2 - - - -
84A ARG* 2.8 62.2 + - + +
85A LEU* 4.3 2.9 - - + +
87A GLN* 1.3 78.7 - - + +
89A ILE* 1.3 61.8 + - + +
91A LEU* 3.7 10.4 - - + +
92A ILE* 3.2 31.8 + - + +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 4.0 34.1 - - + -
23A ALA* 5.6 2.7 - - + -
24A ILE* 4.4 14.8 - - + -
63A ILE* 4.6 8.5 - - + -
65A VAL* 3.8 27.6 - - + -
85A LEU* 2.9 31.4 + - + +
86A THR 4.2 1.6 - - - +
88A GLU* 1.3 74.4 - - + +
90A ALA* 1.3 66.7 + - - +
92A ILE* 3.3 6.7 + - + +
93A LEU* 3.0 45.1 + - + +
100A VAL* 4.1 19.3 - - + -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A THR 3.0 20.2 + - - +
87A GLN 3.7 2.2 - - - +
88A GLU 3.4 0.2 - - - -
89A ILE* 1.3 75.1 - - - +
91A LEU* 1.3 58.0 + - - +
93A LEU 3.6 0.2 - - - -
94A GLY* 2.8 24.4 + - - -
95A ILE* 2.9 40.0 + - + +
96A PRO 4.0 3.1 - - - +
97A ASN* 3.4 27.6 - - - +
100A VAL* 4.2 3.5 - - + +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 5.1 1.4 + - - -
87A GLN* 3.0 25.3 + - + +
88A GLU* 3.7 9.4 - - + +
90A ALA* 1.3 74.5 - - - +
92A ILE* 1.3 68.2 + - + +
94A GLY* 3.2 12.2 + - - -
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 4.1 14.5 - - + +
19A ARG* 3.6 81.4 + - + +
20A ILE* 3.9 26.7 - - + +
23A ALA* 4.1 13.7 - - + -
88A GLU* 3.2 18.9 + - + +
89A ILE* 3.3 4.9 + - + +
91A LEU* 1.3 77.8 - - + +
93A LEU* 1.3 59.6 + - - +
94A GLY* 4.7 0.2 - - - -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 3.1 39.4 + - - +
12A ILE* 4.0 30.3 - - + -
16A ALA* 4.1 12.6 - - + -
20A ILE* 4.1 14.8 - - + -
63A ILE* 3.8 35.7 - - + -
89A ILE* 3.0 30.6 + - + +
92A ILE* 1.3 75.7 - - - +
94A GLY* 1.3 63.1 + - - +
95A ILE* 3.9 17.0 - - + -
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 4.9 0.5 + - - -
90A ALA 2.8 6.8 + - - -
91A LEU* 3.2 11.3 + - - -
92A ILE 3.3 0.8 + - - -
93A LEU* 1.3 80.1 - - - +
95A ILE* 1.3 60.1 + - - +
96A PRO* 4.9 0.2 - - - +
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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