Contacts of the helix formed by residues 80 - 99 (chain A) in PDB entry 5I4A
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ILE* 5.9 0.2 - - - +
75A ILE* 4.0 16.4 - - + +
76A LYS 3.3 3.5 + - - +
77A GLU* 3.3 9.2 + - - +
78A GLU 3.2 1.6 - - - -
79A GLU* 1.3 81.7 - - - +
81A LYS* 1.3 63.2 + - - +
82A LYS* 3.4 9.4 + - - +
83A LEU* 3.0 42.5 + - + +
84A PHE* 3.4 16.6 + - - +
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Residues in contact with LYS 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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77A GLU* 3.0 42.6 + - - +
78A GLU* 4.7 5.8 + - - +
80A ASP* 1.3 70.1 + - - +
82A LYS* 1.3 69.3 + - + +
84A PHE* 3.2 4.9 + - - +
85A VAL* 3.1 27.1 + - + +
136A ASN* 2.8 29.5 + - - +
139A ASN* 5.6 3.9 + - - -
141A TYR* 3.7 5.0 + - - +
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Residues in contact with LYS 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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80A ASP* 3.4 6.8 + - - +
81A LYS* 1.3 79.1 - - + +
83A LEU* 1.3 57.4 + - - +
85A VAL* 3.3 6.2 + - - +
86A LYS* 2.8 33.2 + - - +
518A ARG* 6.0 0.7 - - - +
520A ILE* 5.7 9.6 - - - +
11B A 5.6 0.3 - - - +
12B C 4.4 27.8 - - - +
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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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14A ILE* 4.4 12.1 - - + -
16A ARG* 4.2 13.2 - - - +
51A GLU* 3.3 28.5 - - + +
75A ILE* 4.1 33.4 - - + -
80A ASP* 3.0 34.5 + - - +
82A LYS* 1.3 78.1 - - - +
84A PHE* 1.3 53.9 + - - +
86A LYS* 3.8 15.2 - - + +
87A THR* 2.6 47.2 + - - +
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Residues in contact with PHE 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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8A ILE* 5.2 0.4 - - + -
10A ILE* 3.8 26.2 - - + -
11A PRO 3.6 21.3 - - - -
12A LYS* 3.9 20.9 - - + -
13A LYS* 4.0 8.5 - - - -
14A ILE* 3.6 32.1 - - + +
77A GLU* 3.7 21.3 - - + -
80A ASP 3.4 6.6 + - - +
81A LYS 3.2 9.3 + - - +
83A LEU* 1.3 80.0 - - - +
85A VAL* 1.3 60.1 + - - +
87A THR* 3.4 2.1 + - - -
88A LEU* 2.9 45.1 + - + +
141A TYR* 3.9 43.1 - + - -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.1 18.8 + - + +
82A LYS* 3.8 6.3 - - - +
84A PHE* 1.3 74.1 - - - +
86A LYS* 1.3 67.2 + - - +
88A LEU* 3.3 5.4 + - - +
89A TYR* 2.9 49.8 + - + -
134A ILE* 4.4 12.6 - - + +
141A TYR* 3.6 32.5 - - + +
11B A 4.2 13.0 - - - +
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Residues in contact with LYS 86 (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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49A TRP* 6.3 0.8 - - - -
51A GLU* 4.6 12.0 + - - -
82A LYS 2.8 22.3 + - - +
83A LEU* 3.8 15.8 - - + +
85A VAL* 1.3 74.8 - - - +
87A THR* 1.3 63.8 + - - +
89A TYR* 3.3 2.3 + - - +
90A LYS* 3.0 47.7 + - + +
11B A 4.0 37.4 + - - +
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Residues in contact with THR 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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14A ILE* 3.6 22.2 - - + +
39A PHE* 4.3 0.8 - - + -
51A GLU* 3.3 28.9 + - - +
52A ILE* 3.5 24.9 - - - -
53A PRO* 3.7 6.1 - - + -
83A LEU* 2.6 36.9 + - - +
84A PHE 3.7 0.2 - - - -
86A LYS* 1.3 76.6 - - - +
88A LEU* 1.3 59.2 + - - +
90A LYS* 3.3 9.2 + - - +
91A TYR* 2.9 27.4 + - - +
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Residues in contact with LEU 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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8A ILE* 3.6 35.0 - - + -
10A ILE* 3.8 23.1 - - + -
14A ILE* 5.4 0.4 - - - +
53A PRO* 4.9 4.0 - - + -
84A PHE* 2.9 39.6 + - + +
85A VAL* 3.8 4.0 - - - +
87A THR* 1.3 75.7 - - - +
89A TYR* 1.3 57.2 + - - +
91A TYR* 3.2 11.3 + - + +
92A ILE* 2.9 39.7 + - + +
134A ILE* 3.8 20.6 - - + -
141A TYR* 5.2 0.4 - - + -
247A ILE* 4.4 23.8 - - + -
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Residues in contact with TYR 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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85A VAL* 2.9 39.2 + - + +
86A LYS 3.6 3.6 - - - +
87A THR 3.3 0.2 - - - -
88A LEU* 1.3 76.7 - - - +
90A LYS* 1.3 61.8 + - - +
92A ILE* 3.3 10.1 + - + +
93A LYS* 3.0 23.2 + - - +
107A ASN* 3.2 31.0 - - - +
109A PHE* 5.6 0.5 - - - -
132A ILE* 4.1 9.6 - - + -
133A LYS* 3.4 13.7 - - - +
134A ILE* 2.8 45.0 + - + +
11B A 3.2 71.9 + + + -
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Residues in contact with LYS 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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38A ASN 4.7 1.4 - - - +
39A PHE* 3.6 37.7 - - + -
40A LYS* 3.0 46.4 + - - +
51A GLU* 5.2 7.3 + - - +
86A LYS* 3.0 44.4 + - + +
87A THR* 3.7 4.0 - - - +
89A TYR* 1.3 74.0 - - - +
91A TYR* 1.3 57.8 + - - +
93A LYS* 3.4 11.2 + - + +
94A LYS* 3.0 23.4 + - - +
11B A 3.7 18.6 - - + +
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Residues in contact with TYR 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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39A PHE* 3.6 7.5 - + + -
53A PRO* 3.7 25.1 - - + -
55A ILE* 3.4 32.8 - - + +
56A ASP 4.5 2.0 + - - -
57A PHE* 3.9 28.3 - + - -
87A THR 2.9 17.1 + - - +
88A LEU* 3.2 10.3 + - + +
90A LYS* 1.3 75.1 - - - +
92A ILE* 1.3 65.6 + - - +
94A LYS* 3.4 7.9 + - + +
95A LEU* 3.2 44.9 + - + +
246A LYS* 3.2 31.3 + - + +
247A ILE* 3.6 31.2 - - + -
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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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88A LEU* 2.9 39.2 + - + +
89A TYR* 3.3 8.7 + - + +
91A TYR* 1.3 74.0 - - + +
93A LYS* 1.3 67.3 + - - +
95A LEU* 3.2 8.4 + - - +
96A PHE* 3.1 48.5 + - + -
109A PHE* 4.2 10.3 - - + -
132A ILE* 4.2 11.9 - - + -
134A ILE* 4.1 7.0 - - + -
143A LEU* 3.5 31.6 - - + -
244A LEU* 4.8 4.5 - - + -
247A ILE* 3.7 24.2 - - + -
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Residues in contact with LYS 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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38A ASN 5.2 3.4 - - - +
89A TYR 3.0 13.4 + - - +
90A LYS* 3.6 13.7 - - + +
91A TYR 3.3 0.2 - - - -
92A ILE* 1.3 77.7 - - - +
94A LYS* 1.3 56.9 + - - +
96A PHE* 3.3 2.6 + - - +
97A LEU* 2.8 55.2 + - + +
103A PHE* 3.9 40.1 - - + -
107A ASN* 5.5 0.2 - - - +
109A PHE* 3.7 26.2 - - + -
11B A 5.1 13.1 + - - +
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Residues in contact with LYS 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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36A VAL 5.4 0.2 + - - -
37A ASN* 2.7 36.9 + - - +
38A ASN* 3.2 22.2 + - - +
39A PHE* 4.0 5.8 - - + -
57A PHE* 3.6 42.0 - - + -
58A GLN 5.3 4.7 + - - -
90A LYS 3.0 16.2 + - - +
91A TYR* 3.6 13.0 - - + +
92A ILE 3.3 0.4 - - - -
93A LYS* 1.3 76.1 - - - +
95A LEU* 1.3 56.1 + - + +
97A LEU* 3.2 0.7 + - - +
98A ASP* 2.6 69.3 + - - +
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Residues in contact with LEU 95 (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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91A TYR* 3.2 47.6 + - + +
92A ILE* 3.2 8.3 + - - +
94A LYS* 1.3 80.9 - - + +
96A PHE* 1.3 62.1 + - - +
98A ASP* 3.3 11.3 + - + +
99A ASN* 2.6 35.3 + - - +
243A PHE* 3.8 34.3 - - + +
244A LEU* 4.2 14.1 - - + -
246A LYS* 3.7 35.7 - - + +
247A ILE* 5.3 3.6 - - + -
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Residues in contact with PHE 96 (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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92A ILE* 3.1 42.6 + - + -
93A LYS 3.7 3.8 - - - +
95A LEU* 1.3 76.0 - - - +
97A LEU* 1.3 62.7 + - - +
99A ASN 3.0 9.2 + - - -
101A PHE* 3.0 42.3 + + + +
109A PHE* 3.4 55.0 - + + -
130A TYR* 4.7 3.6 - - + -
132A ILE* 3.8 26.2 - - + -
241A LEU* 3.6 31.6 - - + -
243A PHE* 3.7 13.0 - + - -
244A LEU* 4.2 18.8 - - + -
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Residues in contact with LEU 97 (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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38A ASN* 3.7 42.4 + - + +
93A LYS* 2.8 50.0 + - + +
94A LYS 3.7 0.9 - - - +
96A PHE* 1.3 73.2 - - + +
98A ASP* 1.3 57.9 + - - +
100A ASP* 3.0 19.8 + - - +
101A PHE 3.2 21.3 - - - +
102A TYR* 4.6 0.7 - - - -
103A PHE* 4.1 22.7 - - + +
109A PHE* 5.3 1.8 - - + -
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Residues in contact with ASP 98 (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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36A VAL 5.5 0.7 - - - +
37A ASN 4.7 0.5 - - - -
38A ASN* 2.9 24.1 + - - +
94A LYS* 2.6 62.7 + - - +
95A LEU* 3.6 12.5 - - + +
97A LEU* 1.3 73.3 - - - +
99A ASN* 1.3 62.9 + - - +
100A ASP* 3.3 2.4 + - - +
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Residues in contact with ASN 99 (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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95A LEU* 2.6 28.4 + - - +
96A PHE 3.0 5.5 + - - +
98A ASP* 1.3 81.9 - - - +
100A ASP* 1.3 67.9 + - - +
101A PHE* 3.2 14.8 + - + -
243A PHE* 3.2 51.1 - - + +
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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