Contacts of the helix formed by residues 89 - 104 (chain A) in PDB entry 4ECZ
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 LEU 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.3 17.7 - - + -
38A GLN* 4.8 9.4 - - - +
48A ILE* 4.9 1.6 - - + -
80A VAL* 3.8 26.0 - - + -
87A ALA* 4.3 2.9 + - + -
88A ASN* 1.3 73.6 + - - +
90A THR* 1.3 63.8 + - - +
91A LYS 3.3 3.1 - - - -
92A TYR* 3.1 33.0 + - + -
93A ARG* 3.1 39.2 + - + +
114A ILE* 5.5 3.8 - - + -
347A GLU* 5.2 0.4 + - - -
102P DTP 6.2 2.5 - - + +
5T A 3.8 36.3 - - - +
6T T 4.1 10.8 + - - +
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Residues in contact with THR 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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81A ARG* 4.7 13.9 + - - +
88A ASN* 2.5 28.3 + - - -
89A LEU* 1.3 77.4 - - - +
91A LYS* 1.3 57.9 + - - +
93A ARG* 3.2 16.0 + - + +
94A GLU* 2.9 55.6 + - + +
350A GLU* 5.7 0.5 + - - -
351A ARG* 5.0 10.0 - - - +
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Residues in contact with LYS 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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21A VAL* 3.6 25.1 - - + +
22A GLU* 2.9 31.5 + - - +
25A GLN* 2.8 34.8 + - - +
79A GLN 5.6 1.8 + - - -
81A ARG* 6.0 11.1 - - + +
88A ASN 4.9 1.2 + - - +
89A LEU 3.2 1.0 + - - -
90A THR* 1.3 78.2 - - - +
92A TYR* 1.3 67.5 + - + +
94A GLU* 3.6 10.2 + - - +
95A ALA* 3.0 26.0 + - - +
503A GOL 4.7 2.7 + - - -
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Residues in contact with TYR 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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17A PHE* 3.8 6.7 - - + -
18A PHE* 3.5 71.1 - + + -
21A VAL* 3.9 23.6 - - + -
22A GLU* 2.6 30.9 + - - -
36A VAL* 4.0 7.4 - - - +
79A GLN 4.5 0.3 + - - -
80A VAL* 3.9 28.9 - - + -
81A ARG 4.9 1.6 + - - -
88A ASN 4.7 1.8 - - - -
89A LEU* 3.1 30.9 + - + +
91A LYS* 1.3 82.5 + - + +
93A ARG* 1.3 61.3 + - - +
94A GLU 3.2 0.2 - - - -
95A ALA* 3.8 5.5 - - - +
96A SER* 2.9 29.3 + - - -
114A ILE* 3.8 5.1 - - + +
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Residues in contact with ARG 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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89A LEU* 3.1 43.3 + - + +
90A THR* 3.6 15.0 + - + +
92A TYR* 1.3 77.4 - - - +
94A GLU* 1.3 63.7 + - + +
96A SER* 3.3 6.0 + - - -
97A VAL* 3.1 27.1 + - - +
111A ARG* 5.4 7.4 - - - +
114A ILE* 3.7 18.5 - - + +
347A GLU* 4.4 1.8 + - - -
351A ARG* 3.2 43.1 - - - +
6T T 2.7 43.6 + - - -
7T G 3.3 17.0 + - - -
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Residues in contact with GLU 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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90A THR* 2.9 38.6 + - + +
91A LYS* 3.9 8.2 - - - +
93A ARG* 1.3 76.1 - - + +
95A ALA* 1.3 63.8 + - - +
97A VAL* 3.3 17.9 + - + +
98A GLU* 3.3 10.4 + - - +
354A LYS* 4.8 16.3 + - - +
503A GOL 3.1 33.8 + - - +
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Residues in contact with ALA 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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17A PHE* 3.8 6.1 - - + -
21A VAL* 3.7 30.3 - - + -
24A ARG* 4.7 2.0 - - - +
91A LYS 3.0 18.7 + - - +
92A TYR 3.3 3.8 + - - +
94A GLU* 1.3 75.9 - - - +
96A SER* 1.3 62.4 + - - +
98A GLU* 3.2 24.1 + - - +
99A VAL* 3.3 12.3 + - - +
210A PHE* 4.1 13.8 - - + -
503A GOL 3.3 9.1 + - - +
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Residues in contact with SER 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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17A PHE* 3.8 7.8 - - - -
92A TYR 2.9 14.7 + - - -
93A ARG* 3.3 10.5 - - - -
94A GLU 3.2 0.2 - - - -
95A ALA* 1.3 73.2 - - - +
97A VAL* 1.3 66.1 + - - +
99A VAL* 3.1 7.4 + - - +
100A MET* 2.9 39.0 + - - +
111A ARG* 4.2 8.8 + - - -
114A ILE* 2.6 40.3 + - - +
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Residues in contact with VAL 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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93A ARG 3.1 15.7 + - - +
94A GLU* 3.3 11.4 + - - +
96A SER* 1.3 75.2 - - - +
98A GLU* 1.3 63.6 + - + +
100A MET* 3.9 6.7 - - - +
101A GLU* 2.9 52.1 + - + +
315A LEU* 6.2 3.8 - - + -
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Residues in contact with GLU 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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24A ARG* 3.0 40.2 + - - -
94A GLU 3.3 2.2 + - - +
95A ALA* 3.2 14.1 + - - +
97A VAL* 1.3 82.2 - - + +
99A VAL* 1.3 61.7 + - - +
101A GLU* 4.2 6.1 - - - +
102A ILE* 3.4 28.4 + - - +
207A GLU 4.7 2.4 - - - +
208A THR* 4.0 18.5 - - + +
210A PHE* 4.9 0.7 - - - -
503A GOL 2.6 42.5 + - - +
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Residues in contact with VAL 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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14A MET* 3.8 37.0 - - + -
17A PHE* 4.9 2.9 - - + -
95A ALA 3.3 11.6 + - - +
96A SER* 3.1 9.0 + - - +
98A GLU* 1.3 77.4 - - - +
100A MET* 1.3 68.5 + - + +
102A ILE* 3.2 9.9 + - - +
103A MET* 3.1 38.4 + - + +
115A ASP 6.5 0.2 - - - -
204A ILE* 3.9 22.7 - - + -
208A THR* 4.6 3.6 - - + -
210A PHE* 4.0 22.7 - - + -
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Residues in contact with MET 100 (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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96A SER* 2.9 35.6 + - - +
97A VAL* 3.9 6.7 - - - +
99A VAL* 1.3 78.8 - - + +
101A GLU* 1.3 62.3 + - - +
103A MET* 3.4 23.1 + - + -
104A SER* 3.0 27.2 + - - -
109A ILE* 3.7 17.4 - - + +
111A ARG* 4.1 17.5 - - + +
113A SER 3.8 15.0 - - - +
114A ILE 3.9 5.4 - - - +
115A ASP* 4.3 2.2 - - - -
116A GLU 3.6 30.3 - - - +
117A ALA* 3.9 5.2 - - - -
314A GLN* 3.6 19.5 - - + +
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Residues in contact with GLU 101 (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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97A VAL* 2.9 40.6 + - + +
98A GLU* 4.2 5.2 - - - +
100A MET* 1.3 77.2 - - + +
102A ILE* 1.3 64.6 + - + +
104A SER* 3.4 13.9 + - - -
105A ARG* 3.6 11.1 + - - +
314A GLN* 3.8 16.8 - - - +
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Residues in contact with ILE 102 (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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98A GLU 3.4 16.7 + - - +
99A VAL* 3.2 9.3 + - - +
101A GLU* 1.3 77.3 - - + +
103A MET* 1.3 64.2 + - - +
105A ARG* 3.0 36.4 + - - +
106A PHE* 3.5 10.7 - - + -
200A MET 4.8 0.2 - - - +
203A ALA* 4.2 21.8 - - + -
204A ILE* 3.9 24.9 - - + -
207A GLU* 3.7 29.2 - - + +
208A THR* 3.5 27.8 - - + -
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Residues in contact with MET 103 (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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12A VAL* 3.9 33.9 - - - +
99A VAL* 3.1 28.1 + - + +
100A MET* 3.5 28.5 - - + +
102A ILE* 1.3 74.4 - - - +
104A SER* 1.3 57.4 + - - +
106A PHE* 3.0 25.0 + - - +
107A ALA 3.4 8.8 + - - +
109A ILE* 4.0 14.2 - - + +
115A ASP 6.4 0.2 - - - -
116A GLU 5.2 0.2 - - - -
117A ALA* 3.4 31.2 - - + +
119A VAL* 5.2 2.5 - - + -
200A MET* 3.7 27.6 - - + +
204A ILE* 3.7 14.6 - - + -
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Residues in contact with SER 104 (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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100A MET 3.0 17.1 + - - -
101A GLU* 3.5 7.9 - - - -
102A ILE 3.2 0.4 - - - -
103A MET* 1.3 75.9 - - - +
105A ARG* 1.3 60.7 + - - +
106A PHE 3.2 0.8 + - - -
107A ALA 3.4 20.1 + - - +
108A VAL* 6.1 0.4 - - - -
109A ILE* 3.7 11.4 + - - +
314A GLN* 3.2 29.4 + - - -
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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