Contacts of the helix formed by residues 3113 - 3121 (chain E) in PDB entry 1LDK
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 PRO3113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A THR* 3.2 36.8 - - + +
55A SER* 4.8 11.2 - - - +
139A TYR* 5.2 0.4 - - - +
2105D LEU* 4.3 8.7 - - + -
3110E ASP 4.6 1.1 - - - +
3111E SER 2.5 21.5 - - - +
3112E LEU* 1.4 82.0 - - + +
3114E ASP* 1.3 60.8 + - - +
3115E GLU* 2.6 32.3 - - - +
3116E LEU* 4.5 11.6 - - + +
3117E LEU* 2.9 31.1 + - - +
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Residues in contact with ASP3114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A SER 4.9 8.7 + - - +
82A GLN* 3.6 38.7 + - + +
84A VAL* 6.5 0.4 - - + -
3113E PRO* 1.3 75.8 - - - +
3115E GLU* 1.3 71.7 + - + +
3116E LEU 3.3 0.2 - - - -
3117E LEU* 4.5 3.7 - - - +
3118E LEU* 2.7 30.1 + - - +
3138E ARG* 5.3 4.7 - - - -
3141E ARG* 3.8 16.1 + - - -
3142E LEU* 3.3 32.1 - - + +
3146E GLU* 3.9 1.7 - - - +
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Residues in contact with GLU3115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A CYS 3.7 10.3 - - - +
54A THR* 4.4 0.9 - - - -
82A GLN* 3.5 39.5 - - + +
84A VAL* 5.3 6.6 - - + +
139A TYR* 3.1 25.7 + - - -
143A HIS* 3.3 36.1 + - + +
3113E PRO* 2.6 29.3 - - - +
3114E ASP* 1.3 81.2 + - + +
3116E LEU* 1.3 79.1 + - - +
3118E LEU* 3.4 11.2 + - - +
3119E GLY* 3.5 5.2 + - - -
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Residues in contact with LEU3116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS* 5.0 4.7 - - + +
2104D ILE* 3.6 25.4 - - + -
2105D LEU* 3.7 17.9 - - + -
2108D ASN* 3.6 32.1 - - + +
2116D LEU* 3.6 39.0 - - + -
2120D CYS* 4.8 2.9 - - - -
3112E LEU* 4.4 5.6 - - + -
3113E PRO* 4.3 12.1 + - + +
3114E ASP 3.3 0.2 - - - -
3115E GLU* 1.3 88.2 + - - +
3117E LEU* 1.3 57.6 + - - +
3118E LEU 2.9 1.1 - - - -
3119E GLY* 2.4 32.9 + - - -
3120E ILE* 3.5 5.9 + - - +
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Residues in contact with LEU3117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3109E TRP 4.9 2.2 - - - +
3112E LEU* 3.7 27.9 - - + +
3113E PRO 2.9 20.8 + - - +
3114E ASP* 4.2 1.6 - - - +
3116E LEU* 1.3 78.0 - - - +
3118E LEU* 1.3 59.8 + - - +
3119E GLY 3.0 4.9 + - - -
3120E ILE* 3.1 33.8 + - + +
3121E PHE* 3.5 30.4 + - + -
3138E ARG* 4.5 14.8 - - - +
3139E TRP* 4.2 23.8 - - + +
3142E LEU* 3.3 33.9 - - + -
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Residues in contact with LEU3118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLN* 4.2 16.8 - - - +
147A ARG* 4.5 1.8 - - - +
3114E ASP 2.7 23.8 + - - +
3115E GLU 3.4 6.1 - - - +
3116E LEU 2.9 0.2 + - - -
3117E LEU* 1.3 78.5 - - + +
3119E GLY* 1.3 57.5 + - - +
3121E PHE* 4.2 8.5 - - + -
3122E SER* 2.8 19.2 + - - -
3142E LEU* 4.1 25.6 - - + +
3146E GLU* 3.5 39.0 - - + +
3147E SER* 3.9 23.2 + - - +
3148E LEU* 4.2 16.2 - - + -
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Residues in contact with GLY3119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2120D CYS* 3.7 12.5 - - - -
3115E GLU 3.5 3.5 + - - -
3116E LEU 2.4 26.9 + - - -
3118E LEU* 1.3 69.0 - - - +
3120E ILE* 1.3 63.3 + - - +
3121E PHE 3.3 0.2 - - - -
3122E SER* 3.0 21.7 - - - -
3123E CYS* 4.0 6.9 + - - -
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Residues in contact with ILE3120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2104D ILE* 6.3 2.0 - - + -
2120D CYS* 3.5 22.7 - - - +
2123D VAL* 3.2 61.2 - - + +
2124D ALA* 3.4 15.4 - - + +
2127D ILE* 5.8 0.4 - - + -
3112E LEU* 3.8 15.3 - - + -
3116E LEU 4.1 1.6 - - - +
3117E LEU* 3.4 30.5 - - + +
3119E GLY* 1.3 72.8 - - - +
3121E PHE* 1.3 66.2 + - + +
3122E SER 2.7 15.9 + - - -
3123E CYS* 3.0 19.2 + - - +
3124E LEU* 3.8 7.4 - - + +
3139E TRP* 6.6 0.2 - - + -
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Residues in contact with PHE3121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2127D ILE* 5.7 2.0 - - + -
3117E LEU* 3.5 38.1 + - + +
3118E LEU* 4.4 8.5 - - + +
3119E GLY 3.3 0.4 - - - -
3120E ILE* 1.3 84.8 - - + +
3122E SER* 1.3 58.6 + - - +
3123E CYS 3.5 0.7 - - - -
3124E LEU* 3.6 25.3 + - + +
3129E LEU* 3.6 28.0 - - + +
3132E VAL* 4.5 9.2 - - + -
3139E TRP* 3.2 63.5 - + - -
3142E LEU* 4.1 26.9 - - + -
3143E ALA* 4.8 4.5 - - - -
3148E LEU* 3.7 16.1 - - + +
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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