Contacts of the helix formed by residues 100 - 116 (chain A) in PDB entry 3EZB
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 ALA 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLU* 3.6 27.7 + - + +
42A ARG* 5.5 0.7 - - + -
43A PHE* 4.0 32.8 - - + +
93A ILE* 4.1 16.9 - - + +
98A MET 4.0 0.2 + - - -
99A THR* 1.3 71.0 - - - +
101A ASP* 1.3 63.0 + - - +
104A ALA* 2.8 35.9 + - - +
141A ILE* 4.6 10.5 - - + -
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Residues in contact with ASP 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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25A VAL 4.3 3.9 - - - +
26A ILE* 3.7 11.6 - - + +
27A ASP* 3.1 32.4 + - - +
99A THR* 2.4 35.7 + - - -
100A ALA* 1.3 75.8 - - - +
102A ALA* 1.3 64.9 + - - -
105A HIS* 3.4 10.9 + - - +
138A LEU* 3.0 37.1 - - + +
141A ILE* 4.5 14.1 - - + +
142A LEU* 5.4 16.4 - - + +
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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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26A ILE* 4.1 18.6 - - + -
27A ASP 4.2 5.2 - - - +
28A ARG* 5.8 6.1 - - - +
98A MET* 5.0 8.1 - - + -
99A THR* 2.9 23.3 + - - +
101A ASP* 1.3 82.5 + - - +
103A ALA* 1.3 66.4 + - - +
105A HIS* 3.4 5.1 + - - +
106A GLU* 3.2 21.5 + - - +
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Residues in contact with ALA 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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89A ILE* 4.3 3.8 - - - +
92A LEU* 3.9 23.7 - - + +
93A ILE* 3.6 25.6 - - + -
98A MET* 4.1 13.6 - - + +
99A THR 2.6 24.1 + - - +
100A ALA 4.2 0.4 - - - +
102A ALA* 1.3 74.6 - - - +
104A ALA* 1.3 63.7 + - - +
106A GLU* 3.2 14.4 + - - +
107A VAL* 3.4 17.2 + - - +
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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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43A PHE* 3.8 27.8 - - + -
89A ILE* 4.4 17.1 - - + +
100A ALA 2.8 24.8 + - - +
101A ASP* 4.6 1.3 - - - +
103A ALA* 1.3 74.4 - - - +
105A HIS* 1.3 63.1 + - - +
107A VAL* 3.1 12.3 + - - +
108A ILE* 3.4 17.0 + - - +
137A LEU* 4.1 15.3 - - + -
138A LEU* 5.5 1.6 - - + -
141A ILE* 4.8 4.3 - - + -
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Residues in contact with HIS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.8 14.9 - - + +
101A ASP 3.4 18.9 + - - +
102A ALA* 3.4 6.0 + - - +
103A ALA 3.3 0.6 - - - -
104A ALA* 1.3 78.7 - - - +
106A GLU* 1.3 57.7 + - - +
108A ILE* 4.8 3.1 - - + +
109A GLU* 2.7 79.5 + - + +
131A ARG* 6.1 4.9 - - + -
134A GLY* 4.9 13.4 + - - -
135A LYS* 5.7 7.4 - - + -
137A LEU* 6.2 0.7 - - - -
138A LEU* 3.9 28.2 - - + +
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Residues in contact with GLU 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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92A LEU* 4.2 19.2 - - + +
98A MET* 4.0 25.1 - - - +
102A ALA 3.2 10.4 + - - +
103A ALA* 3.5 9.8 - - - +
104A ALA 3.2 1.0 - - - -
105A HIS* 1.3 80.0 - - - +
107A VAL* 1.3 54.3 + - - +
109A GLU* 3.8 9.6 - - - +
110A GLY* 2.5 35.0 + - - -
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Residues in contact with VAL 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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85A LEU* 3.3 31.6 - - + -
88A GLU* 4.2 25.4 - - + +
89A ILE* 3.7 27.8 - - + +
92A LEU* 3.6 20.6 - - + -
103A ALA 3.5 13.9 - - - +
104A ALA 3.1 6.0 + - - +
106A GLU* 1.3 77.1 - - - +
108A ILE* 1.3 63.3 + - + +
110A GLY* 3.2 1.7 + - - -
111A GLN* 3.2 28.7 + - + +
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Residues in contact with ILE 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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80A LEU* 5.0 11.2 - - + -
85A LEU* 3.9 29.2 - - + -
89A ILE* 5.9 4.7 - - + -
104A ALA 3.4 13.7 + - - +
105A HIS* 4.2 3.4 - - - +
107A VAL* 1.3 78.3 - - + +
109A GLU* 1.3 63.2 + - - +
110A GLY 3.4 0.2 + - - -
111A GLN* 3.4 4.0 + - - +
112A ALA* 3.1 21.8 + - - +
130A VAL* 3.7 30.7 - - + +
131A ARG* 4.8 4.7 - - - -
133A ILE* 5.2 4.5 - - + -
134A GLY* 3.7 28.7 - - - +
137A LEU* 4.7 12.1 - - + -
348B PHE* 4.3 11.9 - - + -
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Residues in contact with GLU 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 HIS* 2.7 60.7 + - + +
106A GLU* 3.8 6.0 - - + +
108A ILE* 1.3 80.1 - - - +
110A GLY* 1.3 52.1 + - - +
112A ALA* 3.8 5.8 - - + +
113A SER* 2.6 43.6 + - - +
116A GLU* 5.9 1.6 - - - +
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Residues in contact with GLY 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 GLU* 2.5 26.2 + - - -
107A VAL* 3.2 2.4 + - - -
109A GLU* 1.3 74.5 - - - +
111A GLN* 1.3 67.8 + - - +
113A SER* 3.4 7.1 + - - -
114A ALA* 3.1 19.8 + - - +
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Residues in contact with GLN 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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85A LEU* 5.4 2.0 - - + -
88A GLU* 5.2 10.1 + - - -
107A VAL* 3.2 16.7 + - + +
108A ILE 4.0 2.5 - - - +
110A GLY* 1.3 75.8 + - - +
112A ALA* 1.3 69.9 + - - +
114A ALA* 2.7 22.5 + - - +
115A LEU* 3.0 15.9 + - + +
348B PHE* 3.1 65.9 - - + +
349B LYS* 4.9 6.2 + - - +
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ILE 3.1 16.8 + - - +
109A GLU* 3.8 6.7 - - + +
111A GLN* 1.3 78.5 - - - +
113A SER* 1.3 63.4 + - - +
115A LEU* 3.0 16.3 + - - +
116A GLU* 2.9 27.0 + - - +
127A ALA* 4.5 17.3 - - + +
130A VAL* 4.7 8.8 - - + +
131A ARG* 4.7 24.2 - - + +
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Residues in contact with SER 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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109A GLU* 2.6 30.3 + - - -
110A GLY* 3.5 8.3 - - - -
112A ALA* 1.3 72.6 - - - +
114A ALA* 1.3 63.1 + - - +
116A GLU* 3.1 28.9 + - - +
117A GLU* 3.3 19.3 + - - +
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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 GLY 3.1 11.7 + - - +
111A GLN* 2.7 22.4 + - - +
113A SER* 1.3 73.2 - - - +
115A LEU* 1.3 69.1 + - + +
117A GLU* 3.2 33.8 + - - +
118A LEU* 3.9 5.4 + - - +
352B THR* 5.2 5.8 - - + +
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Residues in contact with LEU 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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111A GLN* 3.4 16.2 - - - +
112A ALA* 3.0 7.5 + - - +
114A ALA* 1.3 77.2 - - + +
116A GLU* 1.3 56.1 + - - +
118A LEU* 2.6 48.0 + - + +
123A LEU 4.8 1.3 - - - +
124A LYS* 5.0 3.9 - - - -
127A ALA* 3.4 37.5 - - + -
130A VAL* 4.7 8.7 - - + -
348B PHE* 3.7 12.6 - - + +
351B GLN* 3.5 41.7 - - + +
352B THR* 3.6 22.4 - - + -
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Residues in contact with GLU 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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109A GLU* 5.9 1.6 - - - +
112A ALA* 2.9 14.2 + - - +
113A SER* 3.1 27.8 + - - +
115A LEU* 1.3 75.7 - - - +
117A GLU* 1.3 64.2 + - + +
118A LEU 3.0 9.9 + - - +
124A LYS* 4.8 36.7 + - + +
127A ALA* 5.4 4.5 - - + -
131A ARG* 2.9 33.1 + - - +
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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
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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