Contacts of the helix formed by residues 131 - 144 (chain A) in PDB entry 1HMU
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A TRP* 3.9 13.9 - - + -
127A TRP* 2.9 51.4 + - + +
129A ASN 3.6 0.8 - - - -
130A GLU* 1.3 85.7 - - - +
132A ALA* 1.3 67.7 + - - +
133A THR 3.5 0.9 - - - -
134A PRO* 3.5 0.9 - - - +
135A GLN* 3.0 41.2 + - - +
175A ASN* 3.9 22.0 - - - +
178A ASP* 3.6 37.5 - - + +
179A ILE* 3.7 13.7 - - + +
182A HIS* 4.1 3.2 - - - -
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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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76A TRP* 6.0 0.9 - - + -
79A ASN* 5.3 11.4 + - - +
127A TRP* 3.3 33.7 + - + -
128A HIS* 3.8 17.5 - - + +
131A ILE* 1.3 81.9 - - - +
133A THR* 1.3 63.9 + - - +
135A GLN* 3.6 5.7 - - - +
136A ALA* 3.0 24.3 + - - +
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Residues in contact with THR 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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76A TRP* 3.4 27.2 - - - -
79A ASN* 5.2 1.0 + - - +
82A LEU* 4.2 9.6 - - + +
116A TRP* 3.9 31.9 - - + +
121A PRO 5.1 2.4 + - - +
128A HIS 2.9 19.6 + - - -
129A ASN* 4.6 4.8 - - - +
132A ALA* 1.3 70.7 - - - +
134A PRO* 1.3 73.7 - - + +
136A ALA* 3.2 2.9 + - - +
137A LEU* 3.0 31.1 + - + +
162A ARG* 6.3 1.6 - - + -
165A ARG* 5.9 4.9 - - - +
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Residues in contact with PRO 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 ASN 3.3 23.8 - - - +
130A GLU 3.9 9.4 - - - +
131A ILE 3.5 12.1 - - - +
133A THR* 1.3 95.7 - - + +
135A GLN* 1.3 60.4 + - - +
137A LEU* 3.8 2.1 - - + +
138A GLY 3.0 18.7 + - - -
162A ARG 5.2 1.6 - - - +
163A MET* 3.5 36.7 - - + +
165A ARG* 4.1 10.3 - - + +
182A HIS* 3.5 30.9 - - + +
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Residues in contact with GLN 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 ILE* 3.0 27.9 + - - +
132A ALA* 3.6 5.8 - - - +
134A PRO* 1.3 78.4 - - - +
136A ALA* 1.3 61.5 + - - +
138A GLY* 3.3 2.1 + - - -
139A GLU* 2.9 40.0 + - - +
178A ASP* 2.9 58.6 + - - +
181A LEU* 3.9 21.6 - - + +
182A HIS* 3.8 14.6 - - + +
185A TYR* 3.8 4.6 - - + -
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Residues in contact with ALA 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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79A ASN* 4.9 4.3 - - - +
82A LEU* 3.8 24.5 - - + -
83A LEU* 6.6 0.2 - - + -
132A ALA 3.0 17.4 + - - +
133A THR 3.2 4.0 + - - +
135A GLN* 1.3 77.0 - - - +
137A LEU* 1.3 62.0 + - - +
139A GLU* 3.2 10.9 + - - +
140A MET* 2.9 40.0 + - - +
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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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82A LEU* 3.4 32.5 - - + -
113A PHE* 5.2 9.9 - - + -
116A TRP* 3.8 22.0 - - + +
133A THR* 3.0 27.5 + - + +
134A PRO* 3.8 4.5 - - + +
136A ALA* 1.3 75.0 - - - +
138A GLY* 1.3 64.3 + - - +
140A MET* 3.8 4.8 - - - +
141A LEU* 2.9 33.9 + - + +
159A LEU* 4.3 28.9 - - + +
162A ARG* 4.7 14.1 - - + +
163A MET* 4.0 21.5 - - + -
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Residues in contact with GLY 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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134A PRO 3.0 11.3 + - - -
135A GLN 3.3 3.1 + - - -
137A LEU* 1.3 77.0 - - - +
139A GLU* 1.3 61.3 + - - +
141A LEU* 3.6 1.2 + - - +
142A ILE* 3.1 29.6 + - - +
163A MET* 3.6 25.1 - - - +
185A TYR* 4.0 17.3 - - - -
189A LEU* 4.1 4.2 - - - +
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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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39A LEU* 3.6 41.1 - - + +
135A GLN* 2.9 33.8 + - - +
136A ALA* 3.6 8.7 - - - +
138A GLY* 1.3 75.5 - - - +
140A MET* 1.3 63.3 + - + +
142A ILE* 3.3 3.3 + - - +
143A LEU* 3.1 28.9 + - + +
181A LEU* 5.1 1.0 - - - +
185A TYR* 3.4 32.4 + - + -
244A LYS* 5.2 4.9 + - - -
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Residues in contact with MET 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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82A LEU* 3.0 48.7 - - + +
85A LEU* 3.5 28.7 - - + -
86A GLU* 3.4 33.4 - - + +
89A ILE* 3.7 13.7 - - + +
113A PHE* 4.0 11.2 - - + -
136A ALA* 2.9 31.2 + - - +
137A LEU* 3.9 3.6 - - - +
139A GLU* 1.3 75.4 - - + +
141A LEU* 1.3 64.6 + - - +
143A LEU* 3.4 9.1 + - - +
144A MET* 3.1 27.0 + - - +
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Residues in contact with LEU 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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113A PHE* 4.0 11.0 - - + -
137A LEU* 2.9 26.7 + - + +
140A MET* 1.3 73.4 - - - +
142A ILE* 1.3 66.4 + - - +
144A MET* 3.3 13.9 + - - +
145A ARG* 3.4 15.8 + - - +
151A LEU* 4.0 22.9 - - + +
156A VAL* 4.7 13.5 - - + +
159A LEU* 3.9 43.5 - - + -
160A THR* 4.4 8.3 - - + -
163A MET* 4.3 9.6 - - - -
189A LEU* 3.9 31.3 - - + +
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Residues in contact with ILE 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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32A MET* 3.9 24.5 - - + +
35A VAL* 4.0 24.9 - - + -
36A MET* 4.3 16.4 - - + +
39A LEU* 4.7 1.1 - - + -
138A GLY 3.1 20.0 + - - +
139A GLU* 3.7 6.1 - - - +
141A LEU* 1.3 77.0 - - - +
143A LEU* 1.3 63.2 + - - +
145A ARG* 3.0 20.1 + - - +
146A TYR* 3.4 6.3 - - + -
185A TYR* 3.8 38.6 - - + +
188A LEU* 4.6 9.4 - - + -
189A LEU* 3.7 20.6 - - + -
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Residues in contact with LEU 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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36A MET* 4.0 17.5 - - + +
39A LEU* 3.5 35.4 - - + -
40A LYS* 4.5 1.8 - - + +
86A GLU* 4.5 12.6 - - + +
89A ILE* 3.8 20.2 - - + -
90A GLN* 3.4 25.1 - - - +
93A ILE* 3.8 30.0 - - + +
139A GLU* 3.1 22.1 + - + +
140A MET* 3.6 12.3 - - - +
141A LEU 3.3 0.2 - - - -
142A ILE* 1.3 76.8 - - - +
144A MET* 1.3 59.4 + - - +
145A ARG 2.9 5.5 + - - -
146A TYR* 3.0 20.8 + - - +
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Residues in contact with MET 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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89A ILE* 3.8 27.6 - - + -
92A TYR* 3.8 38.4 - - + -
93A ILE* 4.6 2.2 - - - -
106A PHE* 4.2 12.1 - - + -
109A ILE* 4.1 16.6 - - + -
113A PHE* 4.3 3.1 - - + -
140A MET 3.1 16.3 + - - +
141A LEU 3.7 5.6 - - - +
142A ILE 3.2 0.4 - - - -
143A LEU* 1.3 77.6 - - - +
145A ARG* 1.3 57.5 + - - +
146A TYR 3.1 3.8 + - - -
147A GLY* 3.8 7.7 + - - -
149A LYS 4.5 7.2 - - - +
150A PRO* 4.9 7.3 - - - +
151A LEU* 3.5 50.7 + - + +
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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