Contacts of the helix formed by residues 81 - 100 (chain A) in PDB entry 1L9X
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 SER 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 5.9 5.2 - - - +
76A VAL* 3.1 31.1 - - - +
77A ASP* 2.6 24.8 + - - +
78A LEU* 4.4 0.5 - - - -
80A ARG* 1.3 83.9 - - - +
82A ASP* 1.3 64.4 + - - +
83A TYR* 3.6 6.7 - - - +
84A ALA* 3.2 19.6 + - - +
85A LYS* 3.2 20.1 + - - +
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Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 4.8 17.2 + - + +
30A TYR* 4.3 12.2 + - + -
52A LEU* 3.7 37.6 - - + +
53A ASP* 6.0 1.1 - - - -
80A ARG 3.8 1.0 + - - +
81A SER* 1.3 70.8 - - - +
83A TYR* 1.3 65.3 + - - +
85A LYS* 3.2 22.1 + - - +
86A VAL* 2.9 28.4 + - - +
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Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.9 15.9 - - + +
16A MET 3.6 7.9 - - - -
17A GLN* 3.5 32.1 - - + -
52A LEU* 3.7 19.5 - - + +
71A PHE* 3.3 24.8 - - + +
72A PRO* 2.7 34.9 + - + -
76A VAL* 4.7 8.5 - - + -
78A LEU* 4.3 15.0 - - + -
81A SER* 3.6 11.2 - - - +
82A ASP* 1.3 80.2 - - - +
84A ALA* 1.3 63.2 + - - +
86A VAL* 3.4 0.7 + - - +
87A ALA* 2.9 30.2 + - + +
111A LEU* 3.6 25.8 - - + -
112A GLY* 3.6 6.8 + - - -
115A GLU* 4.4 14.1 - - + -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.5 30.7 - - - +
79A ARG 5.3 0.7 - - - -
80A ARG 4.9 1.3 - - - +
81A SER* 3.2 19.8 + - - +
83A TYR* 1.3 87.2 - - + +
85A LYS* 1.3 62.4 + - + +
88A LYS* 2.9 26.0 + - - +
115A GLU* 3.7 21.0 - - - +
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 4.6 11.0 - - - +
81A SER 3.3 14.8 - - - +
82A ASP* 3.2 24.4 + - - +
84A ALA* 1.3 78.5 - - + +
86A VAL* 1.3 63.3 + - + +
88A LYS* 3.4 7.0 + - - +
89A ILE* 3.2 28.8 + - + +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.7 16.4 - - + -
50A VAL* 4.4 0.7 - - + -
52A LEU* 3.8 25.6 - - + +
59A TYR* 3.4 41.1 - - + +
82A ASP 2.9 16.3 + - - +
83A TYR 4.0 0.7 - - - +
85A LYS* 1.3 76.3 - - + +
87A ALA* 1.3 66.6 + - - +
89A ILE* 3.1 7.7 + - + +
90A PHE* 3.0 47.3 + - + -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.8 13.2 - - + +
71A PHE* 3.5 27.1 - - + -
83A TYR* 2.9 19.7 + - + +
84A ALA* 3.4 4.9 + - - +
86A VAL* 1.3 76.0 - - - +
88A LYS* 1.3 58.6 + - - +
90A PHE 3.4 0.3 + - - -
91A TYR* 2.8 31.2 + - - +
115A GLU* 3.7 28.0 - - + -
119A LEU* 4.4 1.3 - - - -
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Residues in contact with LYS 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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84A ALA 2.9 17.0 + - - +
85A LYS* 3.6 8.1 - - - +
86A VAL 3.2 0.2 - - - -
87A ALA* 1.3 76.7 - - - +
89A ILE* 1.3 57.2 + - + +
91A TYR* 3.7 0.6 - - - +
92A ASN* 2.9 51.0 + - - +
115A GLU* 4.3 0.6 + - - +
119A LEU* 3.8 30.5 - - + -
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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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56A GLU* 3.5 30.7 - - - +
59A TYR* 3.8 39.5 - - + -
85A LYS* 3.2 17.9 + - + +
86A VAL* 3.1 12.9 + - + +
88A LYS* 1.3 80.0 - - + +
90A PHE* 1.3 64.1 + - + +
92A ASN* 3.5 5.1 + - - +
93A LEU* 3.0 46.1 + - + +
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Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.6 0.2 - - + -
50A VAL* 4.0 5.4 - - + -
59A TYR* 3.6 39.3 - + + -
62A LEU* 4.0 18.6 - - + -
63A PHE* 4.0 34.2 - + + -
66A ILE* 4.0 17.7 - - + -
69A ILE* 3.4 48.5 - - + -
71A PHE* 4.4 3.4 - - + -
86A VAL* 3.0 37.1 + - + +
87A ALA 4.0 2.9 - - - +
89A ILE* 1.3 77.5 - - + +
91A TYR* 1.3 66.4 + - - +
93A LEU* 3.3 6.1 + - + +
94A SER* 2.9 24.3 + - - -
104A PHE* 4.5 1.9 - + + -
106A VAL* 4.9 1.9 - - - +
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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
----------------------------------------------------------
71A PHE* 4.5 4.6 - - + -
87A ALA 2.8 19.0 + - - +
88A LYS 3.7 2.2 - - - +
90A PHE* 1.3 76.8 - - - +
92A ASN* 1.3 78.6 + - - +
94A SER* 2.7 26.4 + - - -
95A ILE* 3.0 37.0 + - + +
106A VAL* 4.9 6.7 - - + -
116A LEU* 4.5 10.8 - - + -
119A LEU* 3.7 44.4 + - + -
120A ILE* 3.4 35.1 - - + +
189A PHE* 3.6 16.3 - + - -
214A VAL* 4.2 14.1 - - + -
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Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LYS* 2.9 47.9 + - - +
89A ILE* 4.0 4.8 - - - +
91A TYR* 1.3 94.1 - - - +
93A LEU* 1.3 64.1 + - + +
95A ILE* 3.3 6.5 + - - +
96A GLN* 3.0 26.1 + - - +
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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
----------------------------------------------------------
56A GLU* 5.0 4.9 - - - +
59A TYR 4.3 2.0 - - - +
60A GLU* 4.3 32.1 - - + +
63A PHE* 3.5 44.5 - - + -
89A ILE* 3.0 39.2 + - + +
90A PHE* 3.7 6.3 - - + +
91A TYR 3.2 0.2 - - - -
92A ASN* 1.3 77.8 - - + +
94A SER* 1.3 58.4 + - - +
96A GLN* 3.6 27.2 + - - +
97A SER* 2.8 31.5 + - - -
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Residues in contact with SER 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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63A PHE* 3.8 4.4 - - - -
90A PHE 2.9 14.1 + - - -
91A TYR* 2.7 20.8 + - - -
93A LEU* 1.3 75.2 - - - +
95A ILE* 1.3 71.7 + - - +
97A SER* 2.9 20.2 + - - -
98A PHE* 3.0 14.0 + - - +
104A PHE* 3.7 30.9 + - - +
106A VAL* 3.7 17.4 - - - +
212A TYR* 4.9 0.6 - - - -
213A PRO* 6.0 0.9 - - - +
214A VAL* 4.8 3.6 - - - +
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Residues in contact with ILE 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* 3.0 54.4 + - + +
92A ASN* 3.8 7.9 - - - +
94A SER* 1.3 84.8 + - - +
96A GLN* 1.3 64.9 + - - +
98A PHE* 3.3 3.6 + - - +
99A ASP* 3.0 33.3 + - - +
189A PHE* 4.5 0.9 - - + -
212A TYR* 3.5 52.5 - - + +
214A VAL* 4.7 0.9 - - + -
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Residues in contact with GLN 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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60A GLU* 5.8 1.2 + - - -
63A PHE* 6.4 0.4 - - - -
92A ASN 3.0 18.1 + - - +
93A LEU* 3.6 25.9 + - - +
95A ILE* 1.3 79.0 - - - +
97A SER* 1.3 62.7 + - - +
99A ASP* 3.3 10.1 + - - +
100A ASP* 2.8 38.4 + - - +
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PHE* 3.6 14.9 - - - -
93A LEU 2.8 20.0 + - - -
94A SER* 2.9 16.8 + - - -
96A GLN* 1.3 71.9 - - - +
98A PHE* 1.3 61.3 + - - +
100A ASP* 2.9 16.2 + - - -
101A GLY 3.1 0.2 + - - -
102A ASP* 2.7 66.9 + - - +
104A PHE* 3.8 3.5 - - - +
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Residues in contact with PHE 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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94A SER 3.0 14.4 + - - +
95A ILE 3.3 4.2 + - - +
97A SER* 1.3 81.5 + - - +
99A ASP* 1.3 63.9 + - - +
101A GLY* 2.8 20.1 + - - -
102A ASP 3.5 9.4 - - - +
103A TYR* 3.8 33.7 - + - -
104A PHE 5.7 0.4 - - - +
211A LYS* 3.4 37.0 - - + -
212A TYR* 3.4 23.8 - + + -
213A PRO* 3.7 19.1 - - + -
146C HIS* 4.9 9.2 - + - -
210C TYR* 3.6 39.4 + + - -
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.0 24.6 + - - +
96A GLN* 3.6 11.1 - - - +
97A SER 3.2 0.2 - - - -
98A PHE* 1.3 79.6 - - - +
100A ASP* 1.3 63.5 + - - +
101A GLY 3.3 1.0 + - - -
211A LYS* 4.6 4.7 + - - -
212A TYR* 2.7 31.4 + - - -
210C TYR* 6.0 1.1 - - - -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 2.8 31.2 + - - +
97A SER* 2.9 12.8 + - - +
99A ASP* 1.3 82.7 - - - +
101A GLY* 1.3 61.0 - - - +
102A ASP* 4.9 3.1 - - + +
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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
------------------------------------------------------------
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