Contacts of the helix formed by residues 124 - 136 (chain A) in PDB entry 2EVT
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 ILE 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A PHE* 3.7 25.5 - - + -
111A ILE* 4.2 13.0 - - + -
123A LEU* 1.3 78.2 - - - +
125A ARG* 1.3 59.5 + - - +
126A VAL 3.4 2.9 - - - +
127A ASN* 3.3 18.7 + - - +
128A ALA* 3.0 27.0 + - - +
155A ALA* 3.8 20.6 - - + -
156A PRO* 3.4 34.2 + - + +
158A LYS* 3.6 31.0 - - + -
161A PHE* 4.3 14.4 - - + -
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Residues in contact with ARG 125 (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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120A HIS* 5.9 1.8 + - - -
123A LEU* 3.6 40.7 - - + +
124A ILE* 1.3 75.8 - - - +
126A VAL* 1.3 62.7 + - + +
128A ALA* 3.8 5.8 - - - +
129A THR* 2.8 37.5 + - - +
152A LEU* 3.9 17.7 - - - +
153A TYR* 3.2 77.3 + - - +
155A ALA* 5.0 7.5 + - + +
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Residues in contact with VAL 126 (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 SER* 5.2 0.4 - - - +
115A GLU* 4.7 1.1 - - + -
116A ARG* 3.7 16.4 - - + +
117A ASP* 3.7 46.4 - - + +
123A LEU 5.6 1.1 - - - +
124A ILE* 5.6 0.4 - - - -
125A ARG* 1.3 75.9 - - + +
127A ASN* 1.3 74.5 + - - +
129A THR* 4.0 4.8 - - - -
130A LYS* 3.0 30.0 + - - +
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Residues in contact with ASN 127 (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 PHE* 3.8 23.0 - - + -
110A SER* 2.7 38.4 + - - +
111A ILE* 3.7 12.9 + - + +
115A GLU* 2.8 26.7 + - - +
116A ARG* 4.9 0.6 - - - +
123A LEU 4.1 4.0 + - - -
124A ILE* 3.4 33.1 - - - +
125A ARG 3.2 0.2 - - - -
126A VAL* 1.3 83.5 - - - +
128A ALA* 1.3 57.4 + - - +
130A LYS* 3.5 4.1 + - - +
131A ALA* 3.1 27.9 + - - +
158A LYS* 4.9 3.4 - - - +
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Residues in contact with ALA 128 (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* 3.5 12.9 - - + -
107A PHE* 3.7 17.5 - - + -
124A ILE 3.0 17.3 + - - +
125A ARG* 3.9 7.0 - - - +
126A VAL 3.3 0.2 - - - -
127A ASN* 1.3 75.4 - - - +
129A THR* 1.3 59.5 + - - +
131A ALA 3.5 0.2 + - - -
132A TYR* 3.0 28.1 + - - +
152A LEU* 4.1 28.1 - - + +
155A ALA* 5.2 5.4 - - + -
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Residues in contact with THR 129 (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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125A ARG* 2.8 24.6 + - - +
126A VAL* 4.0 5.2 - - - -
128A ALA* 1.3 74.3 - - - +
130A LYS* 1.3 66.8 + - - +
132A TYR* 3.7 6.7 - - + +
133A GLU* 2.9 48.8 + - + +
152A LEU* 4.4 14.2 - - + +
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Residues in contact with LYS 130 (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* 4.2 8.5 - - + -
110A SER* 4.0 12.4 - - - +
115A GLU* 2.7 41.4 + - - +
126A VAL 3.0 19.2 + - - +
127A ASN* 3.6 4.7 - - - +
128A ALA 3.4 0.2 - - - -
129A THR* 1.3 76.5 - - - +
131A ALA* 1.3 56.1 + - - +
133A GLU* 3.4 9.6 + - - +
134A MET* 2.7 60.4 + - + +
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Residues in contact with ALA 131 (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* 3.3 44.4 - - + +
106A VAL* 3.7 12.9 - - + +
107A PHE* 3.6 14.4 - - + +
127A ASN 3.1 16.8 + - - +
128A ALA 3.8 0.2 - - - +
129A THR 3.3 0.2 - - - -
130A LYS* 1.3 72.5 - - - +
132A TYR* 1.3 66.3 + - - +
134A MET 3.9 0.5 - - - -
135A ALA* 3.0 30.5 + - - +
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Residues in contact with TYR 132 (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* 3.6 12.0 - + + -
128A ALA 3.0 18.2 + - - +
129A THR* 3.2 5.1 + - + +
131A ALA* 1.3 77.0 - - - +
133A GLU* 1.3 59.6 + - + +
136A LEU* 2.9 35.9 + - + +
137A LYS* 2.9 57.4 + - + -
140A HIS* 3.3 20.8 + - - +
145A GLN* 3.4 31.9 - - + +
148A PHE* 3.6 37.2 - + + +
149A GLN* 5.5 1.6 - - + -
152A LEU* 3.6 24.7 - - + -
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Residues in contact with GLU 133 (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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129A THR* 2.9 39.7 + - + +
130A LYS* 3.8 9.2 - - - +
132A TYR* 1.3 79.7 - - + +
134A MET* 1.3 61.4 - - + +
135A ALA 4.9 0.2 - - - -
136A LEU 4.4 0.2 + - - -
137A LYS* 3.9 43.3 + - + +
138A LYS* 4.7 6.2 + - - +
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Residues in contact with MET 134 (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* 4.5 15.6 + - + +
106A VAL* 3.6 31.9 - - + -
130A LYS* 2.7 56.6 + - + +
131A ALA* 4.5 0.7 - - - +
133A GLU* 1.3 77.3 - - + +
135A ALA* 1.3 58.3 + - - +
139A TYR* 6.1 0.2 - - - -
195A TYR* 5.5 0.7 + - - -
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Residues in contact with ALA 135 (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 ARG* 3.4 40.8 - - - +
102A ARG* 3.8 12.1 - - + -
103A PHE* 3.4 20.4 - - + +
106A VAL* 5.7 0.9 - - + -
131A ALA 3.0 18.3 + - - +
134A MET* 1.3 79.6 - - - +
136A LEU* 1.3 59.9 + - + +
138A LYS* 6.3 0.2 - - - -
139A TYR* 3.7 16.4 - - - -
195A TYR* 4.4 2.4 + - - -
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Residues in contact with LEU 136 (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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45A ILE* 5.2 4.3 - - + -
48A VAL* 4.6 12.6 - - + -
96A TRP* 4.3 15.3 - - + -
99A ARG* 3.7 30.3 - - + +
100A GLY* 4.8 5.2 - - - -
103A PHE* 4.4 23.3 - - + -
132A TYR* 2.9 27.1 + - + +
133A GLU 4.4 0.4 + - - -
135A ALA* 1.3 81.2 - - + +
137A LYS* 1.3 65.1 + - - +
138A LYS 3.2 2.7 - - - -
139A TYR* 2.9 12.7 + - - -
140A HIS* 2.9 38.6 - - + +
148A PHE* 4.1 22.7 - - + -
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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