Contacts of the helix formed by residues 151 - 163 (chain A) in PDB entry 3LMK
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A TRP* 3.4 35.8 + - - -
149A PRO* 3.6 1.1 - - - +
150A GLY* 1.3 76.9 - - - +
152A SER* 1.3 54.9 + - - +
153A SER* 3.7 6.6 + - - -
154A VAL* 3.3 28.2 + - - +
155A ALA* 2.8 34.5 + - - +
174A ALA* 4.2 1.8 - - - -
223A TYR* 5.6 1.2 - - - +
279A GLU* 3.9 9.8 + - - -
506A GLU* 3.4 7.0 + - - -
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Residues in contact with SER 152 (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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151A SER* 1.3 71.8 + - - +
153A SER* 1.3 59.6 + - - +
155A ALA* 3.1 1.9 + - - +
156A ILE* 2.9 35.1 + - - +
174A ALA* 3.6 10.3 - - - +
175A THR 3.2 3.6 + - - -
176A SER* 3.1 37.9 + - - -
179A LEU* 4.1 4.6 - - - +
222A ASN* 4.0 4.5 - - - -
223A TYR* 4.0 10.4 - - - +
506A GLU* 2.8 33.3 + - - -
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Residues in contact with SER 153 (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 SER* 4.1 11.4 + - - -
151A SER* 3.5 6.3 + - - -
152A SER* 1.3 80.6 - - - +
154A VAL* 1.3 64.5 + - - +
156A ILE* 3.6 8.1 - - - +
157A GLN* 3.2 21.3 + - - +
221A GLY* 4.2 8.5 - - - -
222A ASN* 3.5 36.6 + - - +
223A TYR* 4.7 1.0 - - - +
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Residues in contact with VAL 154 (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 SER* 4.9 2.2 - - - -
100A TRP* 4.0 8.5 - - + +
101A HIS 3.9 17.3 - - - +
102A SER* 3.8 27.6 - - - +
105A ALA* 3.4 29.4 - - + -
149A PRO* 3.6 17.9 - - + -
151A SER* 3.3 27.5 + - - +
152A SER 3.2 0.4 - - - -
153A SER* 1.3 79.8 + - - +
155A ALA* 1.3 55.6 + - - +
157A GLN* 3.3 4.2 + - - +
158A VAL* 3.1 26.5 + - - +
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Residues in contact with ALA 155 (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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149A PRO* 3.7 20.1 - - + +
151A SER 2.8 19.8 + - - +
152A SER 3.1 4.7 + - - +
154A VAL* 1.3 69.3 - - - +
156A ILE* 1.3 56.5 + - - +
158A VAL 3.2 0.5 + - - -
159A GLN* 2.8 38.2 + - - +
169A GLN* 3.5 15.0 + - - +
174A ALA* 4.2 13.0 - - + -
179A LEU* 4.5 3.6 - - + -
188A PHE* 4.1 17.5 - - + -
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Residues in contact with ILE 156 (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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152A SER 2.9 16.0 + - - +
153A SER* 3.6 10.1 - - - +
155A ALA* 1.3 76.0 - - - +
157A GLN* 1.3 68.0 + - - +
159A GLN* 3.1 6.9 + - - +
160A ASN* 3.0 38.2 + - - +
178A ASP* 4.7 5.4 - - + -
179A LEU* 4.1 13.0 - - + +
185A PHE* 3.8 32.5 - - + -
222A ASN* 3.4 43.1 - - + +
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Residues in contact with GLN 157 (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 SER* 4.1 30.8 - - - +
106A LEU* 3.8 30.2 - - + +
153A SER 3.2 11.4 + - - +
154A VAL 3.3 9.1 + - - +
156A ILE* 1.3 82.0 - - - +
158A VAL* 1.3 62.8 + - + +
160A ASN* 3.6 7.7 + - - +
161A LEU 3.6 6.9 + - - -
106B LEU* 5.7 0.2 - - - +
157B GLN* 2.7 35.5 + - - +
160B ASN* 2.8 33.7 + - + -
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Residues in contact with VAL 158 (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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40A LEU* 3.9 18.2 - - + -
105A ALA* 3.8 25.4 - - + +
106A LEU* 4.5 2.2 - - - +
109A SER* 3.4 26.9 - - - +
112A PHE* 6.3 0.2 - - + -
146A VAL* 4.8 1.1 - - + -
149A PRO* 4.2 3.6 - - + -
154A VAL 3.1 17.0 + - - +
155A ALA 3.7 3.1 - - - +
156A ILE 3.1 0.2 - - - -
157A GLN* 1.3 74.7 - - + +
159A GLN* 1.3 60.9 + - - +
161A LEU* 3.2 7.1 + - - +
162A LEU* 2.9 44.3 + - + +
169A GLN* 3.7 18.6 - - + +
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Residues in contact with GLN 159 (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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155A ALA 2.8 18.7 + - - +
156A ILE* 3.1 4.0 + - - +
158A VAL* 1.3 72.4 - - - +
160A ASN* 1.3 59.3 + - - +
162A LEU* 4.3 5.6 - - - +
163A GLN* 2.9 50.4 + - - +
169A GLN* 3.0 27.7 + - - +
179A LEU* 5.1 0.2 - - + -
185A PHE* 3.4 34.5 - - + -
187A TYR* 3.1 44.9 + - - +
188A PHE* 3.7 14.2 - - + +
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Residues in contact with ASN 160 (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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156A ILE* 3.0 31.9 + - - +
157A GLN* 3.8 7.2 - - - +
158A VAL 3.3 0.4 - - - -
159A GLN* 1.3 77.4 - - - +
161A LEU* 1.3 59.9 + - - +
163A GLN* 3.6 20.2 + - - +
164A LEU* 3.5 14.4 - - - +
184A LEU 4.4 2.4 + - - -
185A PHE* 3.9 22.6 - - - -
102B SER* 6.4 1.8 - - - -
103B ALA* 5.8 1.4 - - - -
106B LEU* 3.4 18.7 - - + +
157B GLN* 2.8 32.7 + - - +
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Residues in contact with LEU 161 (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 LEU* 4.0 23.3 - - + -
109A SER* 3.6 44.0 - - - +
110A ILE* 3.9 17.9 - - + +
113A ILE* 4.0 13.2 - - + -
157A GLN 3.6 1.8 + - - -
158A VAL 3.2 7.7 + - - +
159A GLN 3.2 0.4 - - - -
160A ASN* 1.3 78.8 - - - +
162A LEU* 1.3 66.7 + - + +
164A LEU* 3.2 20.1 + - - +
165A PHE* 3.4 20.1 - - + -
106B LEU* 4.1 8.7 - - + +
110B ILE* 3.8 31.9 - - + -
161B LEU* 4.9 5.6 - - + -
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Residues in contact with LEU 162 (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 SER* 4.9 6.1 - - - -
112A PHE* 5.0 5.8 - - + -
113A ILE* 4.6 10.5 - - + -
146A VAL* 3.7 39.7 - - + -
158A VAL* 2.9 37.8 + - + +
159A GLN* 3.3 6.5 + - - +
161A LEU* 1.3 86.0 - - + +
163A GLN* 1.3 62.3 + - - +
165A PHE* 3.0 16.3 + - - +
166A ASN 3.3 8.0 + - - -
167A ILE* 3.3 41.9 + - + +
169A GLN* 3.9 17.5 - - + -
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Residues in contact with GLN 163 (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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159A GLN* 2.9 46.2 + - - +
160A ASN* 3.6 21.5 + - - +
162A LEU* 1.3 75.5 - - - +
164A LEU* 1.3 69.9 + - + +
165A PHE 3.3 1.2 + - - -
166A ASN* 3.3 17.8 + - - +
183A THR 5.5 0.7 - - - +
184A LEU 2.8 30.3 + - - +
185A PHE* 3.9 0.6 - - - +
186A LYS* 4.3 4.1 - - + +
187A TYR* 3.9 27.1 - - + +
55B ARG* 4.4 10.1 + - - +
103B ALA* 4.1 19.8 - - - +
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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