Contacts of the helix formed by residues 151 - 163 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B TRP* 3.6 33.6 + - - -
149B PRO* 3.5 1.6 - - - +
150B GLY* 1.3 78.0 - - - +
152B SER* 1.3 61.6 + - - +
153B SER* 3.4 14.6 + - - -
154B VAL* 3.4 24.7 + - - +
155B ALA* 2.8 31.5 + - - +
174B ALA* 4.1 1.8 - - - -
223B TYR* 5.7 0.7 - - - +
279B GLU* 4.5 5.6 + - - -
507B GLU* 3.3 7.6 + - - -
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Residues in contact with SER 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B SER* 1.3 73.3 + - - +
153B SER* 1.3 61.2 + - - +
155B ALA* 3.3 2.1 + - - +
156B ILE* 3.0 28.4 + - - +
174B ALA* 3.6 9.1 - - - +
175B THR 3.3 3.1 + - - -
176B SER* 3.0 39.3 + - - -
179B LEU* 4.2 3.1 - - - +
222B ASN* 4.1 1.1 - - - -
223B TYR* 3.9 15.3 - - - +
507B GLU* 2.4 37.6 + - - -
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B SER* 3.8 6.8 + - - -
151B SER* 3.4 7.1 + - - -
152B SER* 1.3 79.1 - - - +
154B VAL* 1.3 65.2 + - - +
156B ILE* 3.6 8.3 - - - +
157B GLN* 3.2 20.8 + - - +
221B GLY* 4.2 9.1 - - - -
222B ASN* 3.7 32.5 + - - +
223B TYR* 4.7 1.2 + - - +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B SER* 5.1 1.8 - - - -
100B TRP* 4.1 8.3 - - + +
101B HIS* 3.8 26.9 - - - +
102B SER* 3.7 18.6 - - - +
105B ALA* 3.4 30.7 - - + -
149B PRO* 3.6 16.4 - - + -
151B SER* 3.3 26.0 + - - +
152B SER 3.2 0.4 - - - -
153B SER* 1.3 77.0 - - - +
155B ALA* 1.3 66.0 + - - +
157B GLN* 3.1 4.7 + - + +
158B VAL* 2.9 22.0 + - - +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO* 3.6 25.6 - - + +
151B SER 2.8 21.0 + - - +
152B SER 3.6 4.5 - - - +
154B VAL* 1.3 72.6 - - - +
156B ILE* 1.3 51.6 + - - +
158B VAL* 3.1 3.1 + - - +
159B GLN* 2.6 38.4 + - - +
169B GLN* 3.6 2.0 + - - +
174B ALA* 3.9 19.5 - - + -
179B LEU* 4.5 3.4 - - + -
188B PHE* 4.0 17.7 - - + -
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLN* 5.8 0.2 - - - +
152B SER 3.0 16.5 + - - +
153B SER* 3.6 9.9 - - - +
155B ALA* 1.3 76.1 - - - +
157B GLN* 1.3 58.5 + - + +
159B GLN* 3.3 6.1 + - - +
160B ASN* 2.9 47.9 + - - +
178B ASP* 4.7 3.1 - - + -
179B LEU* 3.7 24.7 - - + +
185B PHE* 3.7 25.8 - - + -
222B ASN* 3.4 42.6 - - + +
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Residues in contact with GLN 157 (chain B).
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* 5.0 1.9 - - - +
157A GLN* 2.7 29.5 + - - +
160A ASN* 2.8 30.9 + - - -
102B SER* 4.1 32.6 - - - +
106B LEU* 3.7 34.4 - - + +
153B SER 3.2 9.9 + - - +
154B VAL 3.1 10.0 + - - +
156B ILE* 1.3 82.3 - - + +
158B VAL* 1.3 65.4 + - + +
160B ASN* 3.3 14.3 + - - +
161B LEU 3.5 3.3 + - - -
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.7 23.3 - - + -
105B ALA* 3.8 22.0 - - + +
106B LEU* 4.8 2.0 - - - +
109B SER* 3.6 27.1 - - - +
149B PRO* 3.8 5.8 - - + -
154B VAL 2.9 16.8 + - - +
155B ALA 3.4 6.5 - - - +
157B GLN* 1.3 75.5 - - + +
159B GLN* 1.3 65.0 + - - +
161B LEU* 3.0 16.7 + - - +
162B LEU* 3.1 30.1 + - + +
169B GLN* 3.5 18.6 - - - +
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Residues in contact with GLN 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ALA 2.6 18.1 + - - +
156B ILE* 3.7 7.6 - - - +
158B VAL* 1.3 71.8 - - - +
160B ASN* 1.3 62.7 + - - +
162B LEU* 4.5 6.3 - - - +
163B GLN* 3.1 44.0 + - - +
169B GLN* 3.1 27.2 + - - +
179B LEU* 5.1 0.4 - - + -
185B PHE* 3.5 31.2 - - + -
187B TYR* 3.1 46.4 + - - +
188B PHE* 3.6 15.9 - - + +
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Residues in contact with ASN 160 (chain B).
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* 6.4 0.9 - - - -
103A ALA* 5.9 0.9 - - - -
106A LEU* 3.4 21.8 - - + +
157A GLN* 2.8 32.7 + - + +
156B ILE* 2.9 30.3 + - - +
157B GLN* 3.4 11.3 - - - +
158B VAL 3.2 0.6 - - - -
159B GLN* 1.3 78.3 - - - +
161B LEU* 1.3 59.7 + - - +
163B GLN* 3.8 17.1 + - - +
164B LEU* 3.5 14.7 - - - +
184B LEU 4.5 2.6 + - - -
185B PHE* 3.7 23.6 - - - -
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Residues in contact with LEU 161 (chain B).
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* 4.2 9.6 - - + +
110A ILE* 3.7 32.1 - - + -
161A LEU* 4.9 5.2 - - + -
106B LEU* 4.0 26.5 - - + -
109B SER* 3.6 42.4 - - - +
110B ILE* 3.7 16.6 - - + +
113B ILE* 4.0 13.2 - - + -
157B GLN 3.5 1.4 + - - -
158B VAL 3.0 8.5 + - - +
160B ASN* 1.3 78.1 - - - +
162B LEU* 1.3 67.9 + - + +
164B LEU* 3.0 21.4 + - - +
165B PHE* 3.4 12.4 - - + -
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B SER* 4.7 17.5 - - - +
112B PHE* 5.0 3.6 - - + -
113B ILE* 4.3 20.6 - - + -
146B VAL* 3.8 33.7 - - + -
158B VAL* 3.1 33.0 + - + +
159B GLN* 4.2 5.6 - - - +
161B LEU* 1.3 77.7 - - + +
163B GLN* 1.3 56.9 + - - +
164B LEU 3.0 0.2 - - - -
165B PHE* 2.8 24.0 + - - +
166B ASN 3.2 7.6 + - - -
167B ILE* 3.2 35.6 + - + +
169B GLN* 3.8 18.2 - - + +
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Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 4.1 12.7 + - - +
103A ALA* 3.9 25.1 - - - +
159B GLN* 3.1 43.2 + - - +
160B ASN* 3.8 20.6 + - - +
162B LEU* 1.3 75.5 - - - +
164B LEU* 1.3 66.5 + - + +
165B PHE 3.1 1.8 + - - -
166B ASN* 3.4 18.4 + - - -
183B THR 5.7 1.2 + - - -
184B LEU 2.9 27.5 + - - +
185B PHE* 3.9 2.3 - - - -
186B LYS* 4.2 4.3 + - + +
187B TYR* 4.0 25.0 - - + +
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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