Contacts of the helix formed by residues 95 - 112 (chain A) in PDB entry 1EF1
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 GLN 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY 3.1 24.4 + - - -
40A ARG* 2.9 51.3 + - - +
41A GLU* 2.8 25.2 + - + +
94A ILE* 1.3 78.8 - - + +
96A ASP* 1.3 61.5 + - - +
97A ILE* 3.5 9.6 - - + +
98A THR* 3.5 15.1 + - - +
99A GLN* 3.3 33.3 + - - +
2001A SO4 3.0 26.8 + - - +
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Residues in contact with ASP 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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95A GLN* 1.3 71.3 - - - +
97A ILE* 1.3 66.3 + - - +
99A GLN* 3.5 10.0 + - - +
100A ARG* 3.0 35.4 + - - +
185A GLU* 3.2 35.4 - - - +
2001A SO4 3.2 25.1 + - - +
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Residues in contact with ILE 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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13A ASP* 5.0 2.9 - - - +
37A ILE* 3.9 32.3 - - + +
38A GLY 3.8 22.2 - - - +
39A LEU* 4.2 8.1 - - + -
95A GLN* 3.8 17.5 - - + +
96A ASP* 1.3 80.4 - - - +
98A THR* 1.3 63.1 + - - +
100A ARG* 3.1 37.3 + - - +
101A LEU* 3.0 53.8 + - + +
2001A SO4 3.9 5.2 + - - +
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Residues in contact with THR 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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39A LEU* 3.2 21.3 - - - +
41A GLU* 3.2 37.2 + - + +
44A PHE* 4.7 0.7 - - + -
45A PHE* 4.2 18.4 - - + -
93A LEU* 3.5 29.4 - - + -
95A GLN* 3.5 13.5 + - - +
96A ASP 3.3 0.4 - - - -
97A ILE* 1.3 74.1 - - - +
99A GLN* 1.3 66.2 + - - +
101A LEU* 3.5 4.8 + - - +
102A PHE* 3.1 26.9 + - + -
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Residues in contact with GLN 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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89A VAL* 6.3 0.2 - - - -
90A SER* 6.2 0.2 - - - +
93A LEU* 3.0 43.2 + - + +
94A ILE 4.6 4.8 + - - -
95A GLN 3.3 18.0 + - - +
96A ASP* 4.0 10.1 + - - +
97A ILE 3.4 0.2 - - - -
98A THR* 1.3 75.5 - - - +
100A ARG* 1.3 60.1 + - - +
102A PHE 3.4 0.2 + - - -
103A PHE* 2.9 31.5 + - - +
185A GLU* 4.2 6.1 - - - +
188A VAL* 4.1 11.0 - - + +
189A LEU* 3.5 46.6 + - - +
192A LEU* 3.6 7.7 - - + +
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Residues in contact with ARG 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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13A ASP* 3.0 24.8 + - - -
96A ASP* 3.0 36.1 + - - +
97A ILE* 3.1 36.3 - - - +
99A GLN* 1.3 76.6 - - - +
101A LEU* 1.3 52.9 + - + +
103A PHE* 3.1 11.5 + - + +
104A LEU* 2.8 55.0 + - + +
188A VAL* 4.4 9.8 - - + +
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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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11A THR* 4.2 4.7 - - - -
12A MSE 3.7 33.6 - - + +
13A ASP* 3.9 22.7 - - - +
37A ILE* 4.2 14.1 - - + -
39A LEU* 4.9 2.9 - - + -
45A PHE* 4.0 20.0 - - + -
80A PHE* 3.8 33.4 - - + +
97A ILE* 3.0 34.9 + - + +
98A THR* 3.9 3.6 - - - +
99A GLN 3.3 0.2 - - - -
100A ARG* 1.3 77.2 - - + +
102A PHE* 1.3 61.2 + - - +
104A LEU* 3.5 0.8 + - + -
105A GLN* 3.1 25.8 + - - +
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Residues in contact with PHE 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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44A PHE* 3.9 17.9 - + + -
45A PHE* 4.0 13.2 - + - -
82A ALA* 3.6 22.7 - - + -
84A PHE 3.1 25.1 - - - -
85A TYR* 3.7 29.4 - + - -
86A PRO* 3.5 15.9 - - + -
89A VAL* 5.9 0.2 - - + -
93A LEU* 3.5 44.0 - - + -
98A THR* 3.1 20.3 + - + +
99A GLN 3.8 2.9 - - - +
101A LEU* 1.3 73.8 - - - +
103A PHE* 1.3 57.0 + - - +
105A GLN* 3.3 5.6 + - + +
106A VAL* 2.8 43.3 + - + +
192A LEU* 4.1 9.0 - - + -
201A TYR* 4.7 3.4 - - - -
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Residues in contact with PHE 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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99A GLN 2.9 19.3 + - - +
100A ARG* 3.4 6.1 - - + +
102A PHE* 1.3 77.9 - - - +
104A LEU* 1.3 85.3 + - + +
106A VAL* 3.9 0.6 - - - +
107A LYS* 2.8 54.2 + - + +
128A TYR 5.5 0.2 - - - -
129A ALA* 4.1 17.5 - - + -
132A SER* 4.3 12.3 - - - -
188A VAL* 3.6 34.8 - - + -
191A TYR* 3.5 53.2 - + + -
192A LEU* 3.8 13.4 - - + +
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Residues in contact with LEU 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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12A MSE 3.3 38.8 - - + +
13A ASP* 3.6 37.7 - - + +
100A ARG* 2.8 33.9 + - + +
101A LEU* 5.2 0.7 - - + -
103A PHE* 1.3 98.5 - - + +
105A GLN* 1.3 62.6 + - - +
107A LYS* 3.8 17.4 + - - +
108A GLU* 3.1 18.4 + - - +
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Residues in contact with GLN 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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12A MSE 3.8 17.1 - - + +
45A PHE* 5.3 1.0 - - - -
81A ARG* 3.6 43.8 + - - +
82A ALA* 2.9 49.1 + - - +
85A TYR* 3.1 27.8 + - + +
101A LEU 3.1 18.0 + - - +
102A PHE* 3.9 4.9 - - + +
104A LEU* 1.3 76.3 - - - +
106A VAL* 1.3 65.3 + - + +
108A GLU* 3.4 5.8 + - - +
109A GLY* 3.2 17.2 + - - -
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Residues in contact with VAL 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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85A TYR* 4.1 20.2 - - + +
102A PHE* 2.8 27.1 + - + +
103A PHE 3.9 2.0 - - - +
105A GLN* 1.3 70.5 - - + +
107A LYS* 1.3 66.2 + - - +
109A GLY* 3.0 5.2 + - - +
110A ILE* 2.9 30.2 + - + +
115A ILE* 4.0 9.5 - - + +
191A TYR* 4.2 5.6 - - + -
192A LEU* 4.2 11.9 - - + -
195A ALA* 3.8 29.2 - - + -
201A TYR* 3.6 30.5 - - + +
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Residues in contact with LYS 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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103A PHE* 2.8 45.0 + - + +
104A LEU* 3.8 17.7 + - - +
106A VAL* 1.3 78.5 - - - +
108A GLU* 1.3 55.8 + - - +
110A ILE* 3.1 1.9 + - - +
111A LEU* 2.8 58.9 + - + +
129A ALA* 3.9 25.4 - - + -
151A LYS 5.2 2.7 + - - +
191A TYR* 3.1 27.8 - - + +
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Residues in contact with GLU 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 MSE 3.7 21.0 - - + +
81A ARG* 3.0 33.0 + - - -
104A LEU 3.1 18.7 + - - +
105A GLN 3.4 5.2 - - - +
106A VAL 3.2 0.2 - - - -
107A LYS* 1.3 77.9 - - - +
109A GLY* 1.3 57.2 + - - +
111A LEU* 3.5 7.1 + - - +
112A ASN* 3.0 43.6 + - - +
114A ASP* 5.5 1.8 - - - +
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Residues in contact with GLY 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 GLN 3.2 7.2 + - - -
106A VAL 3.0 7.7 + - - -
108A GLU* 1.3 77.3 - - - +
110A ILE* 1.3 64.9 + - - +
113A ASP 3.1 2.8 + - - -
114A ASP* 2.9 48.8 + - - -
115A ILE* 3.3 14.7 + - - -
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Residues in contact with ILE 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 VAL* 2.9 30.4 + - + +
107A LYS 3.5 6.5 - - - +
109A GLY* 1.3 74.7 - - - +
111A LEU* 1.3 69.3 + - + +
113A ASP* 3.1 13.5 + - - -
115A ILE* 4.1 26.0 - - + +
117A CYS* 4.1 22.0 - - + -
122A ALA* 5.4 2.5 - - + -
125A LEU* 3.5 28.9 - - + -
154A PRO* 3.4 21.6 - - + +
156A ARG* 5.2 0.3 + - - -
191A TYR* 3.6 16.4 - - - +
195A ALA* 4.0 8.7 - - + -
198A LEU* 4.1 10.3 - - + -
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Residues in contact with LEU 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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107A LYS* 2.8 53.4 + - + +
108A GLU* 3.9 6.5 - - - +
110A ILE* 1.3 78.4 - - + +
112A ASN* 1.3 59.6 + - - +
113A ASP 3.3 0.4 - - - -
151A LYS* 3.2 58.0 + - + +
152A LEU 3.6 32.3 - - - +
153A LEU* 3.6 14.8 - - - +
154A PRO* 3.5 16.7 - - + +
155A GLN 4.4 1.4 + - - -
191A TYR* 5.3 0.9 - - - +
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Residues in contact with ASN 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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108A GLU* 3.0 35.8 + - - +
110A ILE 3.2 0.2 - - - -
111A LEU* 1.3 79.0 - - - +
113A ASP* 1.3 68.9 + - - +
114A ASP* 3.3 21.6 + - - +
151A LYS* 3.9 17.4 - - - +
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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
------------------------------------------------------------
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