Contacts of the helix formed by residues 1004 - 1012 (chain B) in PDB entry 2LP8
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 VAL1004 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.5 32.8 - - + -
71A GLN* 4.1 7.2 - - + +
72A LEU* 3.7 33.7 - - + -
85A GLN* 3.6 22.2 - - + +
86A VAL* 3.8 5.1 - - + +
106A PHE* 4.3 0.7 - - + -
1002B GLY 3.1 13.7 - - - +
1003B CYS* 1.3 80.2 - - - +
1005B GLY* 1.3 63.2 + - - +
1006B ARG 3.2 0.2 - - - -
1007B ALA* 3.3 7.7 - - - +
1008B LEU* 2.6 52.1 + - + +
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Residues in contact with GLY1005 (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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85A GLN* 3.4 15.7 - - - +
86A VAL* 3.3 25.3 - - - +
89A GLU* 2.9 22.5 - - - +
1003B CYS 2.6 8.8 + - - -
1004B VAL* 1.3 81.0 - - - +
1006B ARG* 1.3 56.4 + - - -
1009B ALA* 2.9 16.8 + - - +
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Residues in contact with ARG1006 (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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89A GLU* 2.6 35.2 + - - -
92A ARG* 3.9 10.3 - - - +
1003B CYS* 2.9 18.5 + - - +
1005B GLY* 1.3 71.2 - - - -
1007B ALA* 1.3 62.5 + - - +
1009B ALA* 3.4 6.1 - - - +
1010B ALA* 3.1 25.3 + - - +
1100B 33B 3.7 17.2 - - + +
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Residues in contact with ALA1007 (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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64A ALA* 6.0 1.1 - - + -
68A LEU* 5.4 5.2 - - + -
1003B CYS* 4.2 0.2 - - + -
1004B VAL* 3.1 18.6 + - + +
1006B ARG* 1.3 79.3 - - - +
1008B LEU* 1.3 58.9 + - + +
1010B ALA* 3.2 1.0 + - - +
1011B PHE* 2.7 47.9 + - + -
1100B 33B 3.2 44.6 - - + +
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Residues in contact with LEU1008 (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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57A PHE* 3.5 27.9 - - + -
61A TYR* 3.9 23.6 - - + -
68A LEU* 4.6 3.6 - - + -
86A VAL* 3.2 29.4 - - + -
90A LEU* 4.2 10.8 - - + +
106A PHE* 4.0 27.6 - - + -
1004B VAL* 2.6 55.9 + - + +
1007B ALA* 1.3 77.4 - - + +
1009B ALA* 1.3 58.3 + - - +
1010B ALA 3.1 0.2 - - - -
1011B PHE* 4.4 3.1 - - + +
1012B GLY* 2.8 29.7 + - - +
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Residues in contact with ALA1009 (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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86A VAL* 4.9 0.8 - - - +
89A GLU* 3.1 30.2 - - + +
90A LEU* 4.7 9.3 - - - +
93A ASP* 4.2 21.4 - - + +
1005B GLY 2.9 22.5 + - - +
1006B ARG* 3.4 7.9 - - - +
1008B LEU* 1.3 79.6 - - - +
1010B ALA* 1.3 60.8 + - - +
1012B GLY* 3.9 2.8 + - - -
1013B ASP* 3.9 8.8 + - - +
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Residues in contact with ALA1010 (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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93A ASP* 5.8 0.2 - - - -
1006B ARG 3.1 16.0 + - - +
1007B ALA 3.5 1.8 - - - +
1009B ALA* 1.3 76.6 - - - +
1011B PHE* 1.3 62.8 + - - +
1012B GLY 3.0 5.6 + - - -
1013B ASP* 3.0 20.1 + - - +
1014B CYS* 3.9 0.9 - - - -
1100B 33B 2.6 55.0 - - + +
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Residues in contact with PHE1011 (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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57A PHE* 3.9 18.7 - - + -
60A ARG* 4.3 29.5 - - + +
61A TYR* 5.1 8.5 - - + -
63A ARG* 5.8 10.8 - - - -
64A ALA* 6.0 3.1 - - + -
1007B ALA* 2.7 35.0 + - + +
1008B LEU* 4.6 5.8 - - + -
1010B ALA* 1.3 72.5 - - - +
1012B GLY* 1.3 59.5 + - - +
1013B ASP 3.3 0.4 - - - -
1014B CYS* 3.3 24.6 + - - +
1015B ILE* 4.7 0.3 - - - +
1100B 33B 2.8 89.5 - + - -
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Residues in contact with GLY1012 (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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57A PHE* 3.6 17.4 - - - -
90A LEU* 5.1 3.1 - - - -
99A ARG* 4.7 12.8 - - - +
102A ALA* 4.7 4.0 - - - -
1008B LEU 2.8 21.2 + - - -
1009B ALA 4.3 1.6 - - - -
1010B ALA 3.0 0.2 - - - -
1011B PHE* 1.3 75.5 - - - +
1013B ASP* 1.3 56.1 + - - +
1014B CYS 2.9 9.8 + - - -
1015B ILE* 3.2 24.6 + - - +
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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