Contacts of the helix formed by residues 134 - 148 (chain A) in PDB entry 1IAL
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 SER 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A LYS 4.0 0.8 + - - -
131A THR 4.0 5.2 + - - -
132A ASP 3.8 2.8 + - - -
133A CYS* 1.3 74.0 - - - +
135A PRO* 1.3 76.5 - - - +
137A GLN* 2.9 27.9 + - - +
138A PHE* 2.9 11.3 + - - +
175A HIS* 3.6 39.7 + - - -
177A HIS* 5.4 3.0 + - - -
178A ILE* 3.4 11.5 - - - +
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Residues in contact with PRO 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.9 23.3 - - + -
133A CYS* 3.2 12.6 - - - -
134A SER* 1.3 100.3 - - - +
136A ILE* 1.3 56.6 + - - +
138A PHE* 3.4 8.6 + - + +
139A GLU* 3.1 31.5 + - + +
177A HIS* 6.0 1.6 - - - +
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Residues in contact with ILE 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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90A LEU* 4.1 16.8 - - + +
93A GLN* 4.1 3.6 - - + -
94A LEU* 3.5 42.1 - - + +
97A THR* 4.2 6.3 - - - +
127A PHE* 3.8 52.7 - - + +
130A LYS* 4.0 10.3 - - + -
133A CYS* 3.1 32.6 + - + +
135A PRO* 1.3 76.9 - - - +
137A GLN* 1.3 66.2 + - - +
139A GLU* 4.4 1.3 - - - +
140A SER* 2.9 28.6 + - - -
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Residues in contact with GLN 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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127A PHE 3.4 12.1 - - - +
128A LEU* 2.9 32.9 + - - +
129A GLY* 3.9 1.8 - - - -
130A LYS 3.3 19.8 - - - +
131A THR* 3.4 31.6 + - - +
133A CYS 4.1 0.4 - - - +
134A SER* 2.9 25.9 + - - +
136A ILE* 1.3 81.1 - - - +
138A PHE* 1.3 57.2 + - - +
140A SER* 3.2 3.9 + - - -
141A ALA* 3.0 31.5 + - - +
170A LEU* 3.6 17.9 - - + +
173A SER* 5.2 1.9 + - - -
175A HIS* 5.4 1.0 - - - -
178A ILE* 4.0 15.5 - - + +
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Residues in contact with PHE 138 (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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101A ARG* 5.2 0.2 - - - -
134A SER 2.9 7.5 + - - +
135A PRO* 3.5 10.8 - - + +
136A ILE 3.2 0.2 - - - -
137A GLN* 1.3 74.0 - - - +
139A GLU* 1.3 76.4 + - - +
141A ALA* 3.2 4.6 + - - +
142A TRP* 2.9 64.0 + + - +
177A HIS* 3.5 55.2 - + + +
178A ILE* 3.7 17.8 - - + +
181A GLN* 3.6 20.0 - - + -
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Residues in contact with GLU 139 (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 LEU* 4.1 13.7 - - + -
97A THR* 3.7 19.5 - - + -
98A GLN* 3.2 32.8 + - + +
101A ARG* 2.7 56.4 + - - +
135A PRO* 3.1 17.9 + - + +
136A ILE* 4.0 3.4 - - - +
137A GLN 3.5 0.2 - - - -
138A PHE* 1.3 88.9 - - + +
140A SER* 1.3 57.4 + - - +
142A TRP* 3.4 5.5 + - - +
143A ALA* 3.0 27.0 + - - +
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Residues in contact with SER 140 (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 THR* 3.6 15.6 - - - +
124A PHE* 3.5 28.9 + - - -
127A PHE* 3.5 13.4 - - - +
128A LEU* 3.4 13.3 + - - +
136A ILE 2.9 21.7 + - - -
137A GLN 3.2 5.2 + - - -
139A GLU* 1.3 75.1 - - - +
141A ALA* 1.3 61.2 + - - +
143A ALA* 3.7 3.7 - - - +
144A LEU* 2.8 35.2 + - - +
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Residues in contact with ALA 141 (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 LEU* 3.6 15.7 - - + -
137A GLN 3.0 20.0 + - - +
138A PHE* 3.5 7.0 - - - +
140A SER* 1.3 77.6 + - - +
142A TRP* 1.3 53.6 + - - +
144A LEU 3.5 0.2 + - - -
145A THR* 2.6 38.9 + - - -
167A PHE* 3.8 16.2 - - + -
170A LEU* 4.5 6.5 - - + -
178A ILE* 4.9 3.1 - - + +
181A GLN* 3.9 19.3 - - + -
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Residues in contact with TRP 142 (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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52A ASN* 3.1 42.0 + - + -
54A SER* 3.1 36.3 - - - -
101A ARG* 3.4 45.8 - - + -
105A SER* 2.8 26.7 + - - -
138A PHE* 2.9 49.9 + + - +
139A GLU 3.6 5.6 - - - +
141A ALA* 1.3 78.0 - - - +
143A ALA* 1.3 61.6 + - - +
145A THR* 3.4 1.9 + - - -
146A ASN* 3.2 24.7 + - - +
181A GLN* 3.5 16.1 - - - +
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Residues in contact with ALA 143 (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 THR 5.0 1.1 - - - +
101A ARG* 4.2 15.4 - - + +
104A LEU* 3.6 24.8 - - + +
124A PHE* 4.1 19.7 - - + -
139A GLU 3.0 18.5 + - - +
140A SER* 3.7 6.5 - - - +
142A TRP* 1.3 74.5 - - - +
144A LEU* 1.3 66.0 + - - +
146A ASN* 3.2 6.0 + - - +
147A ILE* 3.1 26.8 + - - +
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Residues in contact with LEU 144 (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 ILE* 4.2 18.8 - - + -
124A PHE* 3.7 24.2 - - + -
125A VAL* 3.7 34.3 - - + +
128A LEU* 3.7 29.8 - - + -
140A SER 2.8 21.0 + - - +
143A ALA* 1.3 73.1 - - - +
145A THR* 1.3 67.0 + - - +
147A ILE* 3.1 6.2 + - + +
148A ALA* 2.9 26.4 + - - +
158A VAL* 3.9 18.6 - - + +
163A ALA* 4.8 0.4 - - + -
167A PHE* 3.6 19.3 - - + -
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Residues in contact with THR 145 (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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50A ARG 4.6 0.2 - - - +
52A ASN* 4.9 0.7 - - + -
141A ALA 2.6 24.6 + - - -
142A TRP 3.4 7.0 - - - -
144A LEU* 1.3 78.2 - - - +
146A ASN* 1.3 63.9 + - - +
148A ALA* 3.2 2.4 + - - +
149A SER 3.1 11.1 + - - -
167A PHE* 4.5 0.4 - - - -
181A GLN* 3.2 29.1 + - - +
184A TRP* 3.4 40.8 - - + +
185A ALA* 3.4 16.5 - - - +
188A ASN* 3.0 26.4 + - - +
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Residues in contact with ASN 146 (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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51A ARG* 3.6 12.5 - - + +
52A ASN* 2.8 49.4 + - - +
104A LEU* 2.7 43.1 + - + +
105A SER* 3.4 5.1 + - - -
112A ILE* 3.7 13.4 - - + +
142A TRP* 3.2 14.4 + - - +
143A ALA 3.7 7.4 - - - +
144A LEU 3.2 0.2 - - - -
145A THR* 1.3 78.9 - - - +
147A ILE* 1.3 65.3 + - - +
149A SER* 2.7 23.6 + - - -
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Residues in contact with ILE 147 (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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104A LEU* 4.1 17.3 - - + -
112A ILE* 4.0 23.4 - - + +
115A ILE* 4.0 24.9 - - + -
116A ILE* 4.1 13.0 - - + -
121A ILE* 4.1 19.5 - - + -
124A PHE* 4.4 13.9 - - + -
143A ALA 3.1 16.5 + - - +
144A LEU* 3.1 11.0 + - + +
146A ASN* 1.3 75.9 - - - +
148A ALA* 1.3 62.4 + - - +
149A SER 3.1 0.2 - - - -
150A GLY* 3.2 12.0 + - - -
154A GLN* 3.7 23.8 - - - +
158A VAL* 3.5 18.2 - - + -
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Residues in contact with ALA 148 (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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49A LYS* 3.6 7.4 - - - +
144A LEU 2.9 16.3 + - - +
145A THR* 3.5 8.1 - - - +
147A ILE* 1.3 79.2 - - - +
149A SER* 1.3 55.8 + - - +
150A GLY 3.2 1.8 - - - -
155A THR* 2.8 28.9 + - + +
158A VAL* 3.8 23.1 - - + +
185A ALA* 4.7 2.7 - - + +
188A ASN* 3.7 18.9 - - + +
189A ILE* 4.4 13.7 - - + -
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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