Contacts of the helix formed by residues 93 - 112 (chain A) in PDB entry 1ECD
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 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LYS* 5.8 0.2 - - - +
91A GLY 3.5 14.4 - - - +
92A VAL* 1.3 77.0 - - - +
94A HIS* 1.3 67.9 + - - +
95A ASP* 3.5 10.7 + - - +
96A GLN* 3.1 34.3 + - - +
97A LEU* 3.0 24.5 + - - +
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Residues in contact with HIS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL 5.7 1.1 - - - -
93A THR* 1.3 75.1 - - - +
95A ASP* 1.3 59.8 + - - +
97A LEU* 3.3 8.8 + - + +
98A ASN* 2.9 35.6 + - - +
133A PHE* 3.6 55.8 - + + -
136A MET* 2.7 38.5 + - + -
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 5.8 0.2 - - - +
93A THR* 3.8 9.7 + - - +
94A HIS* 1.3 79.9 - - - +
96A GLN* 1.3 58.9 + - + +
98A ASN* 3.3 8.4 + - - +
99A ASN* 3.0 38.8 + - - +
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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
----------------------------------------------------------
31A ASP* 3.7 13.5 - - - +
33A SER* 3.0 39.4 + - - +
34A ILE* 3.6 7.4 - - + +
37A LYS* 3.8 18.4 - - - +
92A VAL* 3.4 14.1 - - - +
93A THR* 3.1 41.5 + - - +
95A ASP* 1.3 80.3 - - + +
97A LEU* 1.3 57.9 + - - +
99A ASN* 3.2 2.8 + - - +
100A PHE 2.9 24.1 + - - -
137A HEM 3.5 25.7 - - + +
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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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83A PHE* 4.3 15.5 - - + -
92A VAL* 3.7 17.7 - - + -
93A THR 3.0 16.6 + - - +
94A HIS* 3.5 10.5 - - + +
96A GLN* 1.3 77.8 - - - +
98A ASN* 1.3 57.6 + - - +
100A PHE* 3.3 5.1 - - + +
101A ARG 3.1 21.5 + - - -
129A PHE* 3.4 29.1 - - + -
132A ILE* 3.8 28.3 - - + -
133A PHE* 3.8 18.2 - - + -
136A MET* 4.5 12.1 - - + -
137A HEM 3.5 27.6 - - + -
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Residues in contact with ASN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A HIS* 2.9 21.4 + - - +
95A ASP* 3.6 8.5 - - - +
97A LEU* 1.3 78.1 + - - +
99A ASN* 1.3 61.1 + - - +
101A ARG* 3.5 20.0 + - - +
102A ALA* 3.0 26.7 + - - +
129A PHE* 5.0 5.9 - - - +
133A PHE* 3.7 25.9 - - - -
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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
----------------------------------------------------------
27A VAL 4.8 0.7 - - - +
30A ALA* 3.7 14.9 + - + +
31A ASP* 2.8 42.5 - - + +
34A ILE* 4.6 2.2 - - + -
95A ASP* 3.0 22.0 + - - +
96A GLN 3.2 4.7 + - - +
98A ASN* 1.3 78.0 + - - +
100A PHE* 1.3 61.5 + - - +
102A ALA* 3.6 9.2 - - - +
103A GLY* 2.8 26.5 + - - -
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Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 5.7 5.2 - - + -
24A LEU* 5.7 3.4 - - + -
27A VAL* 3.5 42.5 - - + +
34A ILE* 4.2 1.5 - - + +
62A ILE* 4.5 18.2 - - + -
63A VAL* 6.3 0.7 - - + -
66A PHE* 4.9 18.8 - + - -
96A GLN 2.9 5.7 + - - -
97A LEU* 3.3 11.9 + - + +
99A ASN* 1.3 77.4 - - - +
101A ARG* 1.3 59.5 + - - +
103A GLY* 3.3 1.2 + - - -
104A PHE* 2.9 37.1 + + + +
129A PHE* 4.5 9.0 - + + -
137A HEM 3.5 69.1 - + + -
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Residues in contact with ARG 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 LEU 3.1 6.5 + - - +
98A ASN* 3.5 21.1 - - - +
100A PHE* 1.3 82.0 - - - +
102A ALA* 1.3 65.2 + - - +
104A PHE* 3.3 5.6 + - - +
105A VAL* 3.0 35.6 + - + +
122A GLY* 4.0 11.9 + - - -
125A LEU* 3.6 45.7 + - + +
126A ASP* 2.9 34.4 + - - +
129A PHE* 3.7 34.6 - - + +
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Residues in contact with ALA 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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30A ALA* 5.1 4.5 - - + -
98A ASN 3.0 17.7 + - - +
99A ASN* 3.6 14.6 - - - +
101A ARG* 1.3 78.4 - - - +
103A GLY* 1.3 59.7 + - - +
105A VAL* 3.4 4.9 + - - +
106A SER* 2.9 28.9 + - - -
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Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.5 31.1 - - - +
27A VAL* 4.4 2.5 - - - -
30A ALA* 4.0 7.3 - - - +
99A ASN 2.8 17.8 + - - -
100A PHE 3.7 1.1 - - - -
102A ALA* 1.3 75.1 - - - +
104A PHE* 1.3 59.3 + - - +
106A SER* 3.4 7.5 + - - -
107A TYR* 2.9 28.1 + - - +
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.5 10.8 - + - -
23A ILE* 4.2 29.2 - - + -
27A VAL* 4.4 5.4 - - + +
66A PHE* 3.7 27.8 - + - -
100A PHE* 2.9 28.2 + + + +
101A ARG* 3.6 5.8 - - - +
103A GLY* 1.3 76.9 - - - +
105A VAL* 1.3 67.9 + - + +
107A TYR* 3.1 8.1 + - + +
108A MET* 2.9 60.5 + - + +
114A PHE* 6.1 0.4 - + - -
121A TRP* 3.6 44.9 - + - -
125A LEU* 4.6 10.3 - - + -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.0 27.8 + - + +
102A ALA* 3.9 4.9 - - - +
104A PHE* 1.3 77.3 - - + +
106A SER* 1.3 63.0 + - - +
108A MET* 3.2 7.6 + - - +
109A LYS* 2.9 46.2 + - + +
114A PHE* 4.2 26.0 - - + -
118A GLU* 5.8 0.2 - - - +
125A LEU* 3.9 26.2 - - + -
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Residues in contact with SER 106 (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 ALA* 5.7 1.3 - - - -
29A LYS* 5.7 2.4 + - - -
102A ALA 2.9 18.4 + - - -
103A GLY* 3.5 8.7 - - - -
105A VAL* 1.3 78.8 - - - +
107A TYR* 1.3 61.0 + - - +
109A LYS* 3.5 7.8 + - - +
110A ALA* 3.1 26.0 + - - +
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Residues in contact with TYR 107 (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 VAL* 3.8 29.7 - - + +
19A ASP* 2.6 39.5 + - - +
22A GLY* 3.4 30.3 - - - -
23A ILE* 3.8 22.9 - - + -
26A ALA* 3.8 13.6 - - + +
103A GLY 2.9 13.8 + - - +
104A PHE* 3.2 12.3 - + - +
106A SER* 1.3 76.5 - - - +
108A MET* 1.3 73.3 - - - +
110A ALA* 3.3 1.0 + - - -
111A HIS* 2.8 68.5 + + + +
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Residues in contact with MET 108 (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 SER* 3.3 35.4 - - - +
16A VAL* 3.8 31.9 - - + -
104A PHE* 2.9 45.3 + - + +
105A VAL* 3.2 7.8 + - - +
107A TYR* 1.3 82.7 - - + +
109A LYS* 1.3 58.5 + - - +
111A HIS* 5.1 0.7 - - - -
112A THR* 2.7 50.2 + - + +
114A PHE* 3.6 22.4 - - + +
121A TRP* 3.9 14.4 - - + +
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Residues in contact with LYS 109 (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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105A VAL* 2.9 30.0 + - + +
106A SER* 3.8 7.2 - - - +
108A MET* 1.3 78.4 - - - +
110A ALA* 1.3 58.4 + - - +
112A THR 3.4 13.7 - - - +
114A PHE* 3.6 30.3 - - + -
118A GLU* 3.9 23.2 + - - -
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Residues in contact with ALA 110 (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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106A SER* 3.1 18.1 + - - +
107A TYR* 3.3 0.9 + - - -
109A LYS* 1.3 76.4 - - - +
111A HIS* 1.3 76.0 + - + +
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Residues in contact with HIS 111 (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 VAL* 4.8 2.6 - - + +
19A ASP* 4.6 4.2 + - - -
22A GLY* 6.1 0.4 - - - -
107A TYR* 2.8 75.9 + + + +
110A ALA* 1.3 95.3 + - + +
112A THR* 1.3 68.3 + - + +
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Residues in contact with THR 112 (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 SER* 5.0 2.2 + - - +
15A LYS* 4.6 26.5 - - + +
16A VAL* 3.5 30.3 - - + -
108A MET* 2.7 32.7 + - + +
109A LYS 3.4 17.3 - - - +
110A ALA 5.0 0.2 - - - -
111A HIS* 1.3 83.7 - - + +
113A ASP* 1.3 61.5 + - - +
114A PHE* 3.1 16.8 + - - +
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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