Contacts of the helix formed by residues 110 - 117 (chain D) in PDB entry 5D4D
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 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D PHE 3.3 11.1 + - - -
105D VAL 3.2 19.0 + - - -
107D ASP 3.2 11.8 + - - -
108D VAL* 3.5 6.1 - - - +
109D PRO* 1.3 70.8 - - - +
111D LYS* 1.3 60.5 + - - +
113D GLY* 2.9 24.8 + - - -
114D THR* 2.9 31.7 + - - -
119D SER 6.5 0.2 - - - -
120D ALA* 5.8 9.0 - - - -
123D LEU* 3.5 12.8 - - - +
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Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PHE* 3.6 18.2 + - + +
107D ASP* 4.4 15.4 + - - +
109D PRO* 4.2 18.3 + - - +
110D SER* 1.3 71.5 + - - +
112D ILE* 1.3 61.6 + - - +
114D THR* 3.3 4.8 + - - -
115D LEU* 2.9 33.3 + - - +
498D VAL* 4.3 26.2 - - + +
512D MET* 3.7 21.3 - - + -
1445D HIS* 5.4 0.4 - - - -
1448D THR* 4.5 5.2 - - - +
1449D GLU* 3.1 43.4 + - - +
1452D ILE* 3.4 28.5 - - + +
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ALA* 4.9 0.7 - - + -
104D PHE* 3.6 15.7 + - + +
105D VAL* 4.0 18.8 - - + -
110D SER* 3.4 1.3 + - - +
111D LYS* 1.3 77.3 - - - +
113D GLY* 1.3 56.8 + - - +
115D LEU* 3.2 3.5 + - - +
116D LEU* 2.9 40.8 + - + +
123D LEU* 3.8 17.9 - - + -
127D LEU* 5.3 1.1 - - + -
461D ILE* 3.6 26.5 - - + -
465D LEU* 4.1 5.4 - - + -
512D MET* 3.7 35.7 - - + +
513D ILE* 3.8 27.6 - - + -
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Residues in contact with GLY 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D SER* 2.9 20.2 + - - -
112D ILE* 1.3 76.7 - - - +
114D THR* 1.3 55.7 + - - +
117D ASP* 3.0 9.0 + - - -
118D LEU* 2.7 50.6 + - - +
119D SER 5.7 0.2 - - - -
123D LEU* 3.6 11.4 - - - +
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Residues in contact with THR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D PRO* 4.3 15.4 + - - +
110D SER 2.9 21.8 + - - -
111D LYS 3.6 4.3 - - - -
112D ILE 3.2 0.2 - - - -
113D GLY* 1.3 73.2 - - - +
115D LEU* 1.3 68.3 + - - +
117D ASP* 3.3 5.6 + - - +
494D LYS 4.1 3.4 - - - +
495D ARG* 3.0 61.8 + - + +
498D VAL* 3.8 24.0 - - + +
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LYS 2.9 18.7 + - - +
112D ILE* 3.7 3.4 - - - +
114D THR* 1.3 77.4 - - + +
116D LEU* 1.3 58.3 + - - +
150D ARG* 5.2 0.2 + - - -
465D LEU* 4.4 6.3 - - + -
468D LEU* 3.7 23.0 - - + +
470D LEU* 4.1 6.5 - - + -
473D LEU* 3.9 9.5 - - + +
495D ARG* 3.2 22.2 + - - +
498D VAL* 3.6 25.6 - - + -
499D VAL* 3.7 30.3 - - + +
502D PHE* 4.2 12.3 - - + -
509D PRO* 3.6 38.4 - - + -
512D MET* 4.5 3.1 - - + -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ILE* 2.9 18.6 + - + +
115D LEU* 1.3 74.7 - - - +
117D ASP* 1.3 71.4 + - - +
118D LEU* 3.8 31.5 - - + +
150D ARG* 2.8 42.0 + - - +
461D ILE* 3.8 31.9 - - + -
464D LEU* 3.7 32.5 - - + +
465D LEU* 3.6 26.2 - - + -
468D LEU* 4.4 7.0 - - + -
495D ARG* 4.8 0.2 - - - -
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Residues in contact with ASP 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D GLY 3.0 7.2 + - - -
114D THR* 3.3 5.3 + - - +
115D LEU 3.2 4.6 - - - -
116D LEU* 1.3 82.5 - - - +
118D LEU* 1.3 65.2 + - - +
122D GLU* 4.5 2.1 - - - +
495D ARG* 3.8 32.9 + - - +
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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