Contacts of the helix formed by residues 120 - 137 (chain A) in PDB entry 1IEV
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 ASP 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A THR* 2.9 21.4 + - - +
119A ARG* 1.3 79.4 - - - +
121A PRO* 1.3 65.9 - - - +
122A TYR* 3.3 18.7 + - - +
123A LEU* 3.4 18.5 + - + +
124A VAL* 3.2 22.5 + - - +
126A ARG* 4.9 1.8 + - - -
173A MET* 3.8 3.4 - - - +
387A LYS* 2.9 29.2 + - + +
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Residues in contact with PRO 121 (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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119A ARG 3.6 9.6 - - - +
120A ASP* 1.3 86.6 - - - +
122A TYR* 1.3 57.4 + - - +
124A VAL* 3.2 4.1 + - + +
125A LYS* 2.8 22.9 + - - +
172A SER* 3.3 48.0 - - - +
173A MET* 4.0 10.5 - - + -
175A GLU* 3.5 21.0 - - + +
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Residues in contact with TYR 122 (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 ASP* 3.2 9.4 + - - +
121A PRO* 1.3 77.2 - - - +
123A LEU* 1.3 61.7 + - - +
125A LYS* 3.3 21.1 + - + +
126A ARG* 2.9 75.4 + - + +
129A GLU* 5.2 3.1 - - - -
175A GLU* 5.6 1.8 - - - -
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Residues in contact with LEU 123 (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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115A LEU* 5.0 2.2 - - + -
118A THR* 3.9 30.5 - - + +
120A ASP* 3.4 21.7 + - + +
122A TYR* 1.3 75.5 - - - +
124A VAL* 1.3 67.6 + - + +
126A ARG* 3.2 16.3 + - - +
127A ILE* 2.9 31.0 + - + +
380A LEU* 3.6 26.2 - - + -
383A GLU* 3.4 26.5 - - - +
384A ALA* 3.9 33.9 - - + +
387A LYS* 4.3 7.6 - - + -
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Residues in contact with VAL 124 (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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115A LEU* 4.3 28.3 - - + -
118A THR* 4.8 3.8 - - - +
120A ASP 3.2 14.8 + - - +
121A PRO* 3.5 9.6 - - + +
123A LEU* 1.3 78.0 - - + +
125A LYS* 1.3 61.4 + - - +
127A ILE* 3.1 8.8 + - + +
128A GLY 3.0 17.0 + - - -
163A TYR* 4.4 9.6 - - + +
173A MET* 3.6 41.5 - - + +
176A LEU* 3.5 26.5 - - + +
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Residues in contact with LYS 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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121A PRO 2.8 13.0 + - - +
122A TYR* 3.5 23.6 - - + +
123A LEU 3.2 0.4 - - - -
124A VAL* 1.3 76.8 - - - +
126A ARG* 1.3 58.4 + - - +
128A GLY 3.3 1.2 + - - -
129A GLU* 2.8 51.1 + - - +
175A GLU* 3.3 45.1 + - - +
178A PRO* 4.1 13.9 - - + +
179A GLY* 3.3 7.0 - - - -
183A ASP* 2.5 40.6 + - - -
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Residues in contact with ARG 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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120A ASP* 4.9 1.6 + - - -
122A TYR* 2.9 62.7 + - + +
123A LEU* 3.2 24.0 + - - +
125A LYS* 1.3 75.1 - - - +
127A ILE* 1.3 61.2 + - - +
129A GLU* 3.3 18.3 + - - +
130A ALA* 3.0 22.2 + - - +
380A LEU* 3.4 31.0 - - + +
383A GLU* 3.1 36.8 + - - -
387A LYS* 4.8 2.4 - - - +
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Residues in contact with ILE 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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98A HIS* 6.2 0.7 - - - -
99A GLY 5.7 0.7 - - - +
109A PHE* 3.4 46.2 - - + -
115A LEU* 3.6 40.8 - - + -
123A LEU* 2.9 21.4 + - + +
124A VAL* 3.1 11.0 + - - +
126A ARG* 1.3 73.2 - - - +
128A GLY* 1.3 57.7 + - - +
130A ALA* 3.1 3.2 + - - +
131A THR* 2.6 47.7 + - - +
176A LEU* 4.7 7.9 - - + -
380A LEU* 3.7 15.5 - - + -
384A ALA* 4.1 11.9 - - + -
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Residues in contact with GLY 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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124A VAL 3.0 10.3 + - - -
125A LYS 3.3 4.0 + - - -
127A ILE* 1.3 79.1 - - - +
129A GLU* 1.3 60.0 + - - +
131A THR* 4.2 3.8 - - - -
132A ALA 3.1 17.3 + - - -
176A LEU* 3.7 20.8 - - - +
179A GLY 3.6 6.1 - - - -
180A LEU* 3.5 27.5 - - - +
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Residues in contact with GLU 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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122A TYR* 5.2 3.6 - - - -
125A LYS* 2.8 49.0 + - - +
126A ARG* 3.6 19.1 - - - +
127A ILE 3.1 0.2 - - - -
128A GLY* 1.3 78.2 - - - +
130A ALA* 1.3 62.0 + - - +
132A ALA* 3.3 3.5 + - - +
133A LEU* 3.3 28.8 + - + +
178A PRO 5.6 0.2 - - - -
179A GLY* 3.5 20.4 - - - +
200A LYS* 4.2 13.3 + - - +
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Residues in contact with ALA 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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109A PHE* 3.8 22.0 - - + -
126A ARG 3.0 12.6 + - - +
127A ILE 3.1 7.6 + - - +
129A GLU* 1.3 76.5 - - - +
131A THR* 1.3 55.8 + - - +
133A LEU* 3.2 9.2 + - - +
134A GLU* 3.0 31.7 + - - +
377A HIS* 3.9 27.5 + - + +
380A LEU* 4.1 7.9 - - + -
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Residues in contact with THR 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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96A ALA* 4.0 18.6 - - + +
99A GLY* 3.9 24.7 + - - +
109A PHE* 3.9 4.4 - - - -
127A ILE* 2.6 38.4 + - - +
128A GLY* 3.8 6.7 - - - -
130A ALA* 1.3 70.6 - - - +
132A ALA* 1.3 61.0 + - - +
134A GLU* 3.2 6.9 + - - +
135A VAL* 2.9 47.8 + - + +
176A LEU* 5.7 1.0 - - - +
180A LEU* 3.7 17.0 - - + -
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Residues in contact with ALA 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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128A GLY 3.1 18.3 + - - +
129A GLU* 3.3 5.6 + - - +
131A THR* 1.3 75.1 - - - +
133A LEU* 1.3 58.2 + - - +
135A VAL* 3.2 2.8 + - - +
136A ARG* 2.8 33.8 + - - +
180A LEU* 3.7 28.9 - - - +
199A ASN 4.0 15.9 - - - +
200A LYS* 4.1 8.1 - - + -
201A VAL* 3.8 14.1 - - + +
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Residues in contact with LEU 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 GLU* 3.3 14.8 + - + +
130A ALA* 3.2 10.4 + - - +
132A ALA* 1.3 77.3 - - - +
134A GLU* 1.3 56.4 + - - +
136A ARG* 3.6 2.3 + - - +
137A ALA 3.0 19.9 + - - -
199A ASN* 3.6 26.0 - - + +
200A LYS* 6.0 0.2 - - + -
368A MET* 3.7 22.1 - - + +
371A GLN* 3.4 41.5 - - - +
374A LYS* 4.2 11.9 - - - +
377A HIS* 4.2 8.7 - - + +
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Residues in contact with GLU 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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100A GLN* 3.7 23.6 + - + +
106A ALA* 3.5 9.5 - - - +
107A THR* 2.8 42.3 + - - +
109A PHE* 5.5 2.7 - - + -
130A ALA 3.0 14.9 + - - +
131A THR* 3.9 5.8 - - - +
132A ALA 3.2 0.4 - - - -
133A LEU* 1.3 74.8 - - - +
135A VAL* 1.3 65.2 + - - +
137A ALA* 3.5 17.5 - - - +
138A THR 3.8 2.1 + - - -
371A GLN* 3.5 5.6 - - - +
372A LEU* 3.6 7.7 - - - +
373A GLY* 2.9 24.6 + - - -
377A HIS* 2.8 36.8 - - + -
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Residues in contact with VAL 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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94A ILE* 4.7 3.1 - - + -
96A ALA* 3.5 32.5 - - + -
100A GLN* 3.8 17.9 - - + +
131A THR* 2.9 27.6 + - + +
132A ALA* 3.5 4.3 - - - +
134A GLU* 1.3 73.3 - - - +
136A ARG* 1.3 59.7 + - - +
137A ALA 3.0 1.1 - - - -
138A THR* 2.8 28.6 + - - -
140A ILE* 3.2 45.9 + - + +
142A TYR 4.8 3.4 - - - +
143A ALA* 4.9 3.4 - - + -
201A VAL* 3.7 15.7 - - + -
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Residues in contact with ARG 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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71A GLN* 3.8 3.1 + - - -
132A ALA 2.8 21.9 + - - +
133A LEU 3.8 0.7 - - - +
135A VAL* 1.3 72.2 - - - +
137A ALA* 1.3 60.3 + - - +
138A THR 3.1 0.2 - - - -
139A GLY* 3.1 16.6 + - - +
140A ILE 3.1 21.7 + - - +
141A GLN* 3.3 38.5 + - - +
195A VAL* 5.2 1.8 - - - +
197A GLY 3.7 11.1 + - - -
198A LYS* 3.0 30.1 + - - +
199A ASN 4.1 5.8 - - - -
200A LYS 2.7 26.0 + - - +
201A VAL* 3.9 6.5 - - + -
356A MET* 4.9 11.7 + - - +
358A LEU* 5.5 1.8 - - - +
361A ASN 4.7 11.9 + - - -
363A TYR 5.4 4.8 + - - -
364A ALA* 6.3 0.4 - - - +
365A ASP* 4.9 2.9 + - - +
368A MET* 3.6 32.5 - - + +
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Residues in contact with ALA 137 (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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67A ALA* 3.4 12.2 - - - +
71A GLN* 2.5 24.1 + - - +
133A LEU 3.0 13.3 + - - +
134A GLU 3.5 12.6 - - - +
135A VAL 3.0 1.0 + - - -
136A ARG* 1.3 77.2 - - - +
138A THR* 1.3 56.4 + - - +
368A MET 2.9 31.2 - - - +
369A ALA* 3.6 4.6 - - - +
372A LEU* 3.6 25.6 - - + +
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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