Contacts of the helix formed by residues 4109 - 4120 (chain D) in PDB entry 1F5T
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 SER4109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3100C GLU* 2.9 22.8 + - - -
3103C ARG* 3.6 8.8 - - - +
4078D LYS* 3.5 2.6 + - - -
4108D MET* 1.3 80.0 - - - +
4110D ASP* 1.3 64.4 + - - +
4111D GLU* 3.4 11.8 - - - +
4112D VAL* 3.1 28.2 + - - +
4113D GLU* 3.1 15.6 + - - +
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Residues in contact with ASP4110 (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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4074D ALA* 5.9 1.1 - - - +
4078D LYS* 2.9 25.0 + - - +
4109D SER* 1.3 71.3 - - - +
4111D GLU* 1.3 69.2 + - - +
4113D GLU* 2.8 27.0 + - - +
4114D ARG* 3.1 35.1 + - - +
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Residues in contact with GLU4111 (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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3092C LEU* 3.5 24.2 - - + +
3093C ASP* 4.1 6.2 + - - +
3096C LYS* 3.5 34.8 - - - +
4109D SER* 3.4 13.2 - - - +
4110D ASP* 1.3 81.9 - - - +
4112D VAL* 1.3 61.7 + - - +
4114D ARG* 3.4 31.8 + - - +
4115D ARG* 3.5 12.0 + - - +
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Residues in contact with VAL4112 (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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3086C LEU* 4.5 4.3 - - + -
3090C ILE* 4.4 18.4 - - + -
3092C LEU* 3.9 22.7 - - + -
3100C GLU* 3.2 29.6 - - + +
3104C TRP* 4.2 21.1 - - + -
4108D MET* 4.3 7.2 - - + -
4109D SER* 3.1 21.6 + - - +
4111D GLU* 1.3 74.6 - - - +
4113D GLU* 1.3 64.6 + - - +
4115D ARG* 3.3 6.9 + - - +
4116D LEU* 2.9 30.6 + - + +
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Residues in contact with GLU4113 (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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4074D ALA* 5.6 0.3 - - - +
4077D ARG* 3.0 48.5 + - - +
4078D LYS* 3.3 33.9 + - + +
4081D LEU* 3.5 25.2 - - + +
4108D MET* 4.6 7.4 - - - +
4109D SER 3.1 9.4 + - - +
4110D ASP* 2.8 25.8 + - - +
4112D VAL* 1.3 77.6 - - - +
4114D ARG* 1.3 65.1 + - + +
4116D LEU* 3.2 5.7 + - - +
4117D VAL* 3.0 20.7 + - - +
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Residues in contact with ARG4114 (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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4110D ASP* 3.1 39.1 + - - +
4111D GLU* 3.9 27.7 + - - +
4113D GLU* 1.3 75.8 - - + +
4115D ARG* 1.3 65.4 + - - +
4117D VAL* 2.6 35.3 - - + +
4118D LYS* 3.5 11.7 + - - +
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Residues in contact with ARG4115 (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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3090C ILE* 3.0 23.5 + - + +
3091C GLY* 2.9 26.4 + - - +
3092C LEU* 4.7 8.3 - - + -
4111D GLU* 3.5 10.3 + - - +
4112D VAL* 3.3 10.9 + - - +
4113D GLU 3.3 0.2 - - - -
4114D ARG* 1.3 77.4 - - - +
4116D LEU* 1.3 53.5 + - - +
4118D LYS* 2.7 44.1 + - - +
4119D VAL* 3.1 34.9 + - - +
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Residues in contact with LEU4116 (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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3090C ILE* 3.9 24.6 - - + +
3104C TRP* 5.6 0.2 - - + -
4081D LEU* 3.6 28.5 - - + +
4085D LEU* 3.7 37.5 - - + -
4089D ILE* 5.5 0.4 - - + -
4108D MET* 4.1 22.7 - - + -
4112D VAL* 2.9 24.1 + - + +
4113D GLU 3.5 4.9 - - - +
4115D ARG* 1.3 76.2 - - - +
4117D VAL* 1.3 52.4 + - - +
4118D LYS 3.1 0.9 - - - -
4119D VAL* 4.5 8.3 - - + -
4120D LEU* 2.7 56.3 + - + +
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Residues in contact with VAL4117 (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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4081D LEU* 4.0 19.5 - - + -
4084D ARG* 4.7 8.5 + - - +
4113D GLU 3.0 10.9 + - - +
4114D ARG* 2.6 30.9 + - + +
4115D ARG 2.9 0.2 + - - -
4116D LEU* 1.3 76.3 - - - +
4118D LYS* 1.3 69.8 + - + +
4120D LEU* 4.6 1.8 - - - -
4121D LYS* 4.2 13.3 + - - +
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Residues in contact with LYS4118 (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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4114D ARG* 3.6 20.4 - - - +
4115D ARG* 2.7 24.1 + - - +
4117D VAL* 1.3 86.7 - - + +
4119D VAL* 1.3 70.5 + - + +
4120D LEU 3.4 0.2 - - - -
4121D LYS* 2.9 21.7 - - - +
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Residues in contact with VAL4119 (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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3089C ILE* 3.2 24.7 - - + +
3090C ILE* 3.5 19.3 - - - +
4089D ILE* 4.2 17.4 - - + +
4115D ARG* 3.2 39.0 - - - +
4116D LEU* 4.4 8.1 - - + +
4118D LYS* 1.3 77.6 - - - +
4120D LEU* 1.3 55.9 + - - +
4121D LYS* 2.7 16.6 + - - +
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Residues in contact with LEU4120 (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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4081D LEU* 3.4 32.5 - - + +
4084D ARG* 3.3 49.1 - - + +
4085D LEU* 3.7 25.1 - - + +
4088D ASP* 4.2 12.4 - - + +
4089D ILE* 4.3 17.5 - - + -
4116D LEU* 2.7 23.3 + - + +
4119D VAL* 1.3 81.7 - - - +
4121D LYS* 1.3 75.2 + - - +
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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