Contacts of the helix formed by residues 121 - 137 (chain A) in PDB entry 1IW1
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A VAL* 4.2 2.4 - - - +
112A ARG* 4.7 3.5 + - - -
116A ILE* 3.0 18.9 + - + +
119A ASN* 4.1 17.6 + - + +
120A VAL* 1.3 70.5 - - - +
122A GLY* 1.3 63.5 + - - +
123A PRO* 3.4 10.6 - - - +
124A ALA* 3.2 25.5 + - + +
125A LEU* 2.9 22.9 + - - +
192A HIS* 2.7 30.5 + - - -
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Residues in contact with GLY 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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63A VAL* 3.8 14.6 - - - -
68A PHE* 3.3 28.0 - - - -
120A VAL 3.2 8.0 + - - -
121A ASP* 1.3 71.5 - - - +
123A PRO* 1.3 71.7 - - - +
125A LEU* 3.1 3.3 + - - +
126A VAL* 3.0 26.3 + - - +
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Residues in contact with PRO 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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68A PHE* 3.6 19.0 - - + -
121A ASP* 3.4 11.7 - - - +
122A GLY* 1.3 89.5 - - - +
124A ALA* 1.3 61.7 + - - +
126A VAL* 3.4 0.9 + - + -
127A ALA* 3.2 17.0 + - - +
185A LEU* 4.6 1.1 - - + -
189A GLN* 3.7 55.6 - - + +
192A HIS* 4.1 9.9 - - + -
193A LEU* 3.4 25.8 - - + +
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Residues in contact with ALA 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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112A ARG* 4.7 0.7 - - - +
116A ILE* 3.7 22.9 - - + -
121A ASP* 3.2 31.6 + - - +
123A PRO* 1.3 78.9 - - - +
125A LEU* 1.3 63.5 + - - +
127A ALA* 3.2 4.2 + - - +
128A HIS* 3.2 25.8 + - - -
192A HIS* 3.8 10.4 - - + +
193A LEU* 5.1 0.2 - - - +
196A GLU* 3.8 21.3 - - + -
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Residues in contact with LEU 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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56A LEU* 4.0 11.9 - - + -
59A ALA* 3.7 29.6 - - + +
60A VAL* 3.7 24.5 - - + +
63A VAL* 3.7 23.1 - - + -
73A LEU* 3.7 39.3 - - + -
113A LEU* 5.6 0.7 - - + -
116A ILE* 3.8 8.7 - - + +
121A ASP 2.9 18.3 + - - +
122A GLY 3.6 4.0 - - - +
124A ALA* 1.3 77.0 - - - +
126A VAL* 1.3 64.9 + - + +
128A HIS* 3.0 6.7 + - + -
129A HIS* 2.9 21.0 + - + -
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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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12A LEU* 5.8 0.2 - - + -
68A PHE* 3.9 8.7 - - + -
69A ALA* 3.8 29.2 - - + -
72A LEU* 3.8 11.4 - - + -
73A LEU* 4.9 1.6 - - + -
122A GLY 3.0 20.0 + - - +
123A PRO 3.8 4.3 - - - +
125A LEU* 1.3 81.7 - - + +
127A ALA* 1.3 63.4 - - - +
129A HIS* 3.3 7.3 + - - +
130A TYR* 2.9 23.9 + - + +
180A LEU* 3.7 29.6 - - + -
183A LEU* 4.1 6.7 - - + -
193A LEU* 3.8 18.6 - - + -
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Residues in contact with ALA 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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123A PRO 3.2 10.2 + - - +
124A ALA 3.4 11.0 - - - +
125A LEU 3.2 0.8 - - - -
126A VAL* 1.3 78.0 - - - +
128A HIS* 1.3 60.4 + - - +
130A TYR* 3.4 5.2 + - - +
131A VAL* 3.1 30.1 + - - +
193A LEU* 3.3 36.1 - - + +
196A GLU* 3.7 8.1 - - + -
197A ALA* 3.6 20.0 - - + +
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Residues in contact with HIS 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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56A LEU* 4.0 19.2 - - + +
109A TYR* 3.8 20.3 + + - +
112A ARG* 4.3 2.6 - - + +
113A LEU* 3.6 17.9 - - + +
116A ILE* 3.4 18.6 - - + +
124A ALA 3.2 20.3 + - - -
125A LEU* 3.0 9.8 + - + +
127A ALA* 1.3 78.6 - - - +
129A HIS* 1.3 62.2 + - - +
131A VAL* 4.0 1.2 - - - +
132A ARG* 3.1 29.5 + - + +
196A GLU* 2.8 32.5 + - + +
200A ALA* 3.6 33.2 - - + +
203A PHE* 4.1 12.3 - + - -
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Residues in contact with HIS 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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56A LEU* 4.4 4.4 - - + +
60A VAL* 3.8 17.5 - - + +
72A LEU* 3.4 24.5 - - - +
73A LEU* 3.5 31.4 - - + +
74A ASP 5.1 0.4 + - - -
77A LEU* 3.5 23.7 - - + +
125A LEU* 2.9 17.8 + - + +
126A VAL* 3.5 9.6 - - - +
128A HIS* 1.3 73.1 - - - +
130A TYR* 1.3 61.8 + - - +
133A TYR* 2.9 68.0 + + - +
176A TYR* 2.8 26.2 + + - +
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Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ALA 5.4 0.9 - - - -
12A LEU* 3.9 47.1 - - + -
13A LYS* 3.6 15.6 - - - -
16A THR* 4.1 12.7 + - + -
126A VAL 2.9 17.1 + - - +
127A ALA* 3.6 3.6 - - - +
129A HIS* 1.3 77.1 - - - +
131A VAL* 1.3 87.0 + - + +
134A LEU* 3.0 51.8 + - + +
176A TYR* 3.1 18.3 + + + +
177A ARG* 6.1 0.4 - - + -
180A LEU* 4.1 13.7 - - + -
201A PHE* 4.7 0.4 - + - -
901A HEM 2.6 53.8 + - + +
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Residues in contact with VAL 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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127A ALA 3.1 17.2 + - - +
128A HIS 4.0 2.0 - - - +
130A TYR* 1.3 87.8 - - + +
132A ARG* 1.3 65.1 + - - +
135A GLY 3.5 8.1 + - - -
197A ALA* 3.8 19.1 - - - +
200A ALA* 3.9 23.3 - - + -
201A PHE* 3.7 35.0 - - + +
204A ASN* 4.2 7.0 - - - +
901A HEM 3.4 39.8 - - + +
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Residues in contact with ARG 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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45A LEU* 6.3 0.4 - - - +
49A ALA* 5.6 2.0 - - - +
52A PHE* 3.8 16.9 - - + -
53A TYR* 2.8 36.0 + - + +
56A LEU* 4.0 22.4 - - + -
109A TYR* 3.3 28.0 - - - +
128A HIS* 3.1 17.2 + - + +
129A HIS 4.4 0.2 - - - +
131A VAL* 1.3 80.3 - - + +
133A TYR* 1.3 59.6 + - - +
135A GLY* 3.2 2.1 + - - -
136A ASP* 2.9 56.9 + - - +
160A PHE* 4.1 6.5 - - - -
204A ASN* 2.8 35.5 + - - +
208A PHE* 5.6 1.4 - - - -
901A HEM 3.4 22.8 - - - +
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Residues in contact with TYR 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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53A TYR* 3.7 16.4 - + - -
56A LEU* 3.9 22.1 - - + +
57A GLU* 2.7 37.6 + - - +
60A VAL* 4.7 2.9 - - + +
77A LEU* 3.2 51.7 + - + -
78A ASN* 4.3 2.6 + - - -
79A ARG* 4.0 1.6 - - + -
129A HIS* 2.9 65.0 + + + +
132A ARG* 1.3 71.2 - - - +
134A LEU* 1.3 68.1 + - - +
136A ASP* 3.1 15.2 + - - +
137A LEU* 3.0 29.7 + - + +
163A PHE* 4.5 6.9 - + - -
176A TYR* 5.3 3.6 - - + -
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Residues in contact with LEU 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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129A HIS 4.0 0.6 + - - -
130A TYR* 3.0 46.9 + - + +
133A TYR* 1.3 77.7 - - - +
135A GLY* 1.3 59.2 + - - +
137A LEU* 3.4 10.7 + - + +
138A SER* 2.7 32.6 + - - -
173A LYS* 3.2 42.8 - - + -
176A TYR* 4.2 25.0 - - + -
177A ARG* 4.2 21.5 - - + +
901A HEM 3.9 20.9 - - + -
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Residues in contact with GLY 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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131A VAL 3.5 5.7 + - - -
132A ARG 3.2 6.7 + - - -
133A TYR 3.2 0.6 - - - -
134A LEU* 1.3 78.4 - - - +
136A ASP* 1.3 58.1 + - - +
138A SER 3.0 8.7 + - - -
139A GLY* 3.0 5.2 + - - -
140A GLY 2.9 21.9 + - - -
901A HEM 3.3 40.9 + - - -
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Residues in contact with ASP 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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53A TYR* 2.4 35.0 + - - -
79A ARG* 4.4 0.3 - - - +
132A ARG* 2.9 36.0 + - - +
133A TYR* 3.1 14.1 + - - +
135A GLY* 1.3 75.5 - - - +
137A LEU* 1.3 56.8 + - - +
138A SER 3.1 2.5 + - - -
140A GLY* 3.4 18.0 - - - -
141A GLN* 2.9 22.1 + - - -
160A PHE* 3.5 21.2 - - + -
161A TYR* 4.6 2.4 - - + -
163A PHE* 3.6 22.4 - - + -
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Residues in contact with LEU 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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77A LEU* 4.4 6.7 - - + -
133A TYR* 3.0 22.0 + - + +
134A LEU* 3.8 20.0 - - + +
135A GLY 3.2 0.4 - - - -
136A ASP* 1.3 75.3 - - - +
138A SER* 1.3 58.6 + - - +
141A GLN* 3.8 9.1 - - - +
163A PHE* 3.5 35.7 - - + -
166A ILE* 4.9 3.8 - - + -
169A LEU* 3.4 44.6 - - + +
172A TYR* 3.9 30.3 - - + -
173A LYS* 3.5 26.6 + - + -
176A TYR* 5.9 1.3 - - + -
901A HEM 4.4 0.5 - - - +
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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