Contacts of the helix formed by residues 97 - 116 (chain A) in PDB entry 1E0W
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 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER 4.2 1.5 + - - -
96A LEU* 1.3 77.0 - - - +
98A GLY* 1.3 69.2 + - - +
99A SER 3.5 0.2 + - - -
100A ALA* 3.4 10.5 + - - +
101A LEU* 3.2 17.5 + - - -
142A ASN* 5.4 3.6 - - - -
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Residues in contact with GLY 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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97A SER* 1.3 76.0 - - - +
99A SER* 1.3 57.4 + - - -
101A LEU* 3.2 5.6 + - - +
102A ARG* 3.0 25.9 + - - +
142A ASN 5.4 0.4 + - - -
145A ARG 5.9 0.2 - - - -
146A SER* 4.2 27.6 - - - +
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Residues in contact with SER 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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97A SER 3.5 0.4 + - - -
98A GLY* 1.3 71.5 - - - -
100A ALA* 1.3 62.7 + - - +
102A ARG* 3.3 9.1 + - - +
103A GLN* 3.1 23.9 + - - +
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Residues in contact with ALA 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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56A ARG* 4.3 9.2 + - - +
96A LEU* 4.2 22.2 - - + +
97A SER 3.4 8.2 + - - +
98A GLY 3.3 0.6 - - - -
99A SER* 1.3 80.3 + - - +
101A LEU* 1.3 63.9 + - - +
103A GLN* 3.5 4.8 + - - +
104A ALA* 3.1 22.9 + - - +
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Residues in contact with LEU 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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93A MET* 3.9 35.2 - - + +
96A LEU* 3.9 15.0 - - + +
97A SER* 3.2 20.1 + - - +
98A GLY 3.2 8.4 + - - +
100A ALA* 1.3 76.6 - - - +
102A ARG* 1.3 60.7 + - - +
104A ALA* 3.2 1.8 + - + +
105A MET* 2.9 28.2 + - + +
142A ASN* 3.4 55.0 - - + +
143A LEU* 3.8 22.9 - - + +
146A SER* 4.7 6.5 - - - -
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Residues in contact with ARG 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 GLY 3.0 13.3 + - - +
99A SER* 3.3 12.8 + - - +
101A LEU* 1.3 76.6 - - - +
103A GLN* 1.3 61.7 + - - +
105A MET* 3.3 15.7 + - - +
106A ILE* 3.0 37.1 + - + +
146A SER* 3.1 40.8 + - - +
149A ASP* 3.1 39.8 + - - -
150A TRP* 3.7 21.7 - - - +
153A VAL* 3.8 29.9 - - - +
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Residues in contact with GLN 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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56A ARG* 4.6 9.4 - - - +
99A SER 3.1 15.7 + - - +
100A ALA* 4.0 4.9 - - - +
101A LEU 3.3 0.2 - - - -
102A ARG* 1.3 76.7 - - - +
104A ALA* 1.3 57.6 + - - +
106A ILE* 3.3 21.3 + - - +
107A ASP* 2.9 59.8 + - - +
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Residues in contact with ALA 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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53A GLU* 4.8 1.7 - - - +
56A ARG* 4.2 16.0 - - - +
92A TRP* 4.0 18.2 - - + -
93A MET* 4.4 7.8 - - + +
96A LEU* 3.8 22.0 - - + -
100A ALA 3.1 17.0 + - - +
101A LEU* 3.6 4.7 - - + +
103A GLN* 1.3 76.3 - - - +
105A MET* 1.3 58.0 + - - +
107A ASP* 3.9 5.8 - - - +
108A HIS* 2.9 30.1 + - - +
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Residues in contact with MET 105 (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 5.6 1.1 - - - +
84A ALA* 4.5 10.3 - - + -
93A MET* 4.8 8.0 - - + +
101A LEU* 2.9 14.7 + - + +
102A ARG* 3.3 22.6 + - - +
104A ALA* 1.3 75.8 - - - +
106A ILE* 1.3 69.1 + - + +
108A HIS* 3.3 6.7 + - - +
109A ILE* 3.1 37.1 + - + +
143A LEU* 3.9 28.9 - - + -
150A TRP* 3.8 35.7 - - - +
153A VAL* 4.0 22.7 - - + -
154A ALA* 4.0 16.8 - - + +
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Residues in contact with ILE 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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102A ARG* 3.0 28.9 + - + +
103A GLN* 3.7 23.3 - - - +
105A MET* 1.3 79.6 - - + +
107A ASP* 1.3 63.7 + - - +
109A ILE* 3.3 5.0 + - - +
110A ASN* 3.0 38.2 + - - +
153A VAL* 4.0 23.8 - - + -
157A THR* 3.9 26.4 - - + +
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Residues in contact with ASP 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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53A GLU* 5.6 4.3 - - - +
56A ARG* 4.4 11.0 + - - +
59A PHE* 3.9 7.7 - - + -
103A GLN* 2.9 50.0 + - - +
104A ALA* 3.9 5.6 - - - +
106A ILE* 1.3 77.2 - - - +
108A HIS* 1.3 57.3 + - - +
110A ASN* 3.5 6.8 + - - +
111A GLY* 3.0 26.3 + - - -
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Residues in contact with HIS 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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47A MET 5.4 1.0 + - - -
48A LYS 5.1 0.8 - - - -
49A ILE* 3.8 31.8 + - + +
52A THR* 3.2 26.4 + - - -
53A GLU* 2.6 43.6 + - + +
59A PHE* 4.0 3.1 - - - -
82A THR 5.1 0.8 + - - -
83A LEU* 3.5 30.4 + - + +
93A MET* 4.6 5.2 - - + -
104A ALA 2.9 18.6 + - - +
105A MET* 3.6 7.2 - - - +
106A ILE 3.3 0.2 - - - -
107A ASP* 1.3 74.2 - - - +
109A ILE* 1.3 66.7 + - - +
111A GLY* 3.4 0.9 + - - -
112A VAL* 3.1 39.5 + - + +
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Residues in contact with ILE 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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83A LEU* 4.2 34.8 - - + +
84A ALA* 5.1 2.5 - - + -
105A MET* 3.1 28.8 + - + +
106A ILE* 3.7 5.6 - - - +
108A HIS* 1.3 74.4 - - - +
110A ASN* 1.3 66.1 + - - +
112A VAL* 4.1 0.2 - - - -
113A MET* 3.0 48.6 + - - +
125A VAL* 5.0 2.0 - - + -
154A ALA* 3.9 37.2 - - + +
157A THR* 3.8 22.0 - - + +
158A ALA* 4.1 9.6 - - + -
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Residues in contact with ASN 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 ILE* 3.0 35.6 + - - +
107A ASP* 4.0 6.6 - - - +
109A ILE* 1.3 76.8 - - - +
111A GLY* 1.3 62.5 + - - +
113A MET* 4.2 0.3 - - - +
114A ALA* 3.1 26.5 + - - +
157A THR* 3.7 16.4 + - - +
160A ALA* 6.2 0.2 - - - +
161A ALA* 3.7 27.0 - - - +
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Residues in contact with GLY 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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59A PHE* 4.0 20.9 - - - -
61A PHE* 3.9 9.7 - - - -
107A ASP 3.0 17.3 + - - -
108A HIS 3.9 0.7 - - - -
110A ASN* 1.3 78.2 - - - +
112A VAL* 1.3 62.7 + - - +
114A ALA* 3.9 4.4 - - - +
115A HIS* 3.5 14.0 + - - +
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Residues in contact with VAL 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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47A MET* 5.3 5.4 - - + +
52A THR* 3.8 19.3 - - + +
59A PHE* 4.1 7.4 - - + -
61A PHE* 4.1 13.7 - - + -
83A LEU* 3.9 12.8 - - + -
108A HIS* 3.1 44.7 + - + +
111A GLY* 1.3 74.1 - - - +
113A MET* 1.3 66.2 + - - +
115A HIS* 3.2 14.6 + - - +
116A TYR* 3.5 19.6 + - + -
123A TRP* 3.7 28.0 - - + -
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Residues in contact with MET 113 (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* 3.8 23.8 - - + -
109A ILE* 3.0 24.6 + - - +
110A ASN 4.5 0.2 - - - +
112A VAL* 1.3 75.3 - - - +
114A ALA* 1.3 61.6 + - - +
116A TYR 3.2 3.2 + - - +
117A LYS* 2.9 24.7 + - - +
123A TRP* 3.7 38.5 + - + +
158A ALA* 3.5 48.5 - - + +
161A ALA* 4.0 16.4 - - + -
162A ASP* 3.8 23.2 - - + +
165A ALA* 4.6 0.7 - - + -
167A LEU* 4.4 7.9 - - + -
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Residues in contact with ALA 114 (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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110A ASN 3.1 20.2 + - - +
111A GLY* 3.9 6.3 - - - +
112A VAL 3.3 0.4 - - - -
113A MET* 1.3 76.6 - - - +
115A HIS* 1.3 62.3 + - - +
116A TYR 3.3 0.7 + - - -
117A LYS* 3.5 18.7 + - - +
161A ALA* 5.5 2.6 - - - +
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Residues in contact with HIS 115 (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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61A PHE* 3.5 46.3 - + + +
65A ASP* 2.9 29.4 + - - -
111A GLY 3.5 3.4 + - - +
112A VAL 3.2 10.4 + - - +
114A ALA* 1.3 79.8 - - - +
116A TYR* 1.3 88.1 + + - +
117A LYS 4.0 0.2 + - - -
119A LYS* 4.3 14.6 + - - +
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Residues in contact with TYR 116 (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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47A MET* 3.9 19.5 - - + -
52A THR* 6.1 0.2 - - + -
61A PHE* 4.2 12.7 - + - -
64A ALA* 3.1 28.7 - - + +
65A ASP* 2.7 29.1 + - - -
68A TYR* 4.1 28.3 - + + -
112A VAL* 3.5 19.2 + - + +
113A MET 3.2 6.0 + - - +
115A HIS* 1.3 93.4 - + - +
117A LYS* 1.3 64.3 + - - +
118A GLY 3.2 1.0 + - - -
119A LYS* 2.9 28.7 + - + +
120A ILE* 3.7 32.7 + - + +
123A TRP* 4.3 15.7 + + + +
162A ASP* 4.1 2.9 - - - +
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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