Contacts of the helix formed by residues 99 - 110 (chain A) in PDB entry 3EA4
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 GLY 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LYS* 1.3 70.8 - - - +
100A ALA* 1.3 52.2 + - - +
102A ILE* 3.1 5.9 + - - +
103A LEU* 2.8 35.0 + - - +
228A VAL* 3.8 17.9 - - - -
231A ILE* 3.5 10.9 - - - +
258A ILE 3.4 17.7 - - - -
259A GLN* 3.2 6.4 + - - -
261A GLN 2.9 12.5 + - - -
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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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98A LYS* 3.1 4.5 - - + -
99A GLY* 1.3 76.3 - - - +
101A ASP* 1.3 57.9 + - - +
103A LEU* 3.4 8.6 + - - +
104A VAL* 3.0 32.4 + - - +
125A GLU* 3.6 40.4 - - + +
126A ILE* 3.9 10.6 - - + +
129A ALA* 3.7 4.3 - - + -
132A ARG* 5.8 0.2 - - - +
259A GLN* 3.0 23.9 + - + +
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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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90A ARG* 4.1 9.0 + - - -
91A PHE* 3.7 34.9 - - + -
97A ARG* 4.1 9.3 - - + +
98A LYS* 3.0 29.2 + - - +
100A ALA* 1.3 76.2 - - - +
102A ILE* 1.3 64.9 + - - +
104A VAL* 3.5 2.4 + - - +
105A GLU* 3.1 23.6 + - - +
129A ALA* 3.6 10.4 - - - +
132A ARG* 2.8 39.8 + - - -
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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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97A ARG* 4.0 17.9 - - + +
98A LYS 3.0 12.0 + - - +
99A GLY* 3.4 7.2 - - - +
101A ASP* 1.3 75.7 - - - +
103A LEU* 1.3 56.8 + - - +
105A GLU* 3.3 4.9 + - - -
106A ALA* 2.8 27.7 + - - +
228A VAL* 4.1 15.5 - - + +
231A ILE* 3.9 18.6 - - + -
232A PRO* 4.0 15.7 - - + -
263A ALA* 3.8 35.0 - - + +
265A PRO* 3.9 39.0 - - + -
267A TRP* 3.6 7.1 - - + -
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Residues in contact with LEU 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 GLY 2.8 19.7 + - - +
100A ALA* 3.5 6.3 - - - +
102A ILE* 1.3 74.2 - - - +
104A VAL* 1.3 64.2 + - + +
106A ALA* 3.2 6.0 - - - +
107A LEU* 3.1 33.1 + - + +
126A ILE* 4.2 28.5 - - + -
165A ILE* 5.6 0.2 - - + -
192A ILE* 4.1 28.3 - - + -
225A VAL* 6.3 0.2 - - + -
231A ILE* 3.7 20.1 - - + +
235A ILE* 4.4 20.8 - - + +
252A VAL* 5.4 0.4 - - + -
254A VAL* 3.8 36.3 - - + -
259A GLN* 6.2 0.2 - - + -
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 4.8 4.9 - - - +
100A ALA 3.0 20.7 + - - +
101A ASP* 3.5 4.7 + - - +
102A ILE 3.3 0.2 - - - -
103A LEU* 1.3 75.8 - - + +
105A GLU* 1.3 58.5 + - - +
107A LEU* 3.0 23.9 + - + +
108A GLU* 3.0 16.2 + - - +
126A ILE* 4.1 13.7 - - + +
129A ALA* 3.6 25.1 - - + +
130A LEU* 3.8 29.8 - - + +
133A SER* 3.9 26.9 - - - -
136A ILE* 4.1 5.4 - - + -
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Residues in contact with GLU 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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87A PHE* 4.1 10.8 - - + -
89A SER* 2.8 30.2 + - - -
90A ARG* 4.3 6.6 + - - +
91A PHE* 4.0 12.2 - - + -
97A ARG* 3.8 10.7 + - - -
101A ASP 3.1 17.8 + - - +
102A ILE* 3.7 4.3 - - - +
104A VAL* 1.3 75.8 - - - +
106A ALA* 1.3 52.4 + - - +
108A GLU* 3.1 16.2 + - - +
109A ARG* 2.8 72.2 + - - +
267A TRP* 3.3 18.9 + - + -
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Residues in contact with ALA 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 ILE 2.8 14.3 + - - +
103A LEU* 3.2 13.2 - - - +
105A GLU* 1.3 77.0 - - - +
107A LEU* 1.3 58.7 + - - +
109A ARG* 3.6 3.9 + - - +
110A GLN* 3.2 28.2 + - - +
231A ILE* 4.8 3.4 - - + -
232A PRO* 4.9 2.9 - - + +
235A ILE* 3.7 30.9 - - + +
267A TRP* 3.7 21.6 - - + -
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Residues in contact with LEU 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 LEU* 3.1 29.3 + - + +
104A VAL* 3.0 14.1 + - + +
106A ALA* 1.3 75.0 - - - +
108A GLU* 1.3 64.6 + - - +
109A ARG 3.2 0.2 - - - -
110A GLN* 3.0 11.6 + - - +
111A GLY 3.3 0.2 + - - -
112A VAL* 3.1 32.9 + - + +
115A VAL* 4.4 21.8 - - + -
130A LEU* 5.1 4.5 - - + -
136A ILE* 4.0 12.3 - - + -
163A ILE* 4.8 3.8 - - + -
165A ILE* 4.8 6.5 - - + -
192A ILE* 4.0 23.6 - - + -
235A ILE* 4.4 8.3 - - + -
239A PHE* 3.7 30.7 - - + -
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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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87A PHE* 4.0 27.0 - - + -
90A ARG* 2.7 34.5 + - - +
104A VAL* 3.0 18.5 + - - +
105A GLU* 3.1 21.0 + - - +
107A LEU* 1.3 75.0 - - - +
109A ARG* 1.3 57.3 + - - +
111A GLY* 3.0 18.2 + - - -
112A VAL 4.4 8.3 - - - -
133A SER* 2.7 21.1 + - - -
134A SER 4.4 1.0 + - - -
135A SER* 3.6 17.0 + - - +
136A ILE* 3.6 14.8 - - + +
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Residues in contact with ARG 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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87A PHE* 3.5 48.0 + - + +
89A SER* 4.3 7.3 - - - -
105A GLU* 2.8 45.0 + - - +
106A ALA* 3.8 6.5 - - - +
107A LEU 3.2 0.2 - - - -
108A GLU* 1.3 77.7 - - - +
110A GLN* 1.3 65.7 + - + +
111A GLY 3.2 1.3 + - - -
267A TRP* 3.3 58.4 - - + +
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Residues in contact with GLN 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 ALA 3.2 15.2 + - - +
107A LEU 3.0 11.4 + - - +
109A ARG* 1.3 80.0 + - - +
111A GLY* 1.3 60.1 + - - +
112A VAL* 3.4 1.7 + - - +
235A ILE* 4.2 4.8 - - + +
236A GLU* 3.8 34.8 + - - +
239A PHE* 3.4 57.2 - - + +
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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