Contacts of the helix formed by residues 4026 - 4034 (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 LEU4026 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4024D THR* 3.0 25.5 + - + +
4025D PRO* 1.3 73.4 - - - +
4027D ARG* 1.3 57.4 + - - +
4028D ALA 4.2 1.6 - - - +
4029D ARG* 2.7 54.6 + - + +
4030D ILE* 3.2 7.5 + - - +
4059D ASP 4.3 5.4 - - - +
4060D ARG* 2.7 57.0 - - + +
4061D SER* 3.4 13.0 - - - +
4062D LEU* 3.6 5.6 - - - -
305E G 4.6 9.2 - - - +
306E C 3.9 13.0 - - - +
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Residues in contact with ARG4027 (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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4026D LEU* 1.3 73.4 - - - +
4028D ALA* 1.3 63.8 + - - +
4030D ILE* 3.0 5.4 + - - +
4031D ALA* 2.9 21.8 + - - +
4038D GLY 5.9 0.2 - - - +
4041D VAL* 3.6 20.1 - - + +
4042D SER* 3.7 26.9 + - - +
4045D VAL* 3.8 28.9 - - + +
4056D VAL* 4.4 19.5 - - - +
4060D ARG* 4.3 19.2 + - - +
4062D LEU* 3.5 19.4 - - + +
306E C 3.4 50.8 + - - +
307E T 3.3 30.2 + - - -
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Residues in contact with ALA4028 (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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4026D LEU* 3.2 0.6 - - + -
4027D ARG* 1.3 73.3 - - - +
4029D ARG* 1.3 69.2 + - - +
4031D ALA* 3.6 8.1 - - - +
4032D GLU* 3.2 27.2 + - - +
4038D GLY* 6.4 0.4 - - - -
305E G 3.8 35.2 - - + +
306E C 2.7 24.6 + - - +
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Residues in contact with ARG4029 (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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4018D LEU* 3.6 37.2 - - + -
4023D VAL* 4.7 10.9 - - + +
4024D THR 4.5 9.3 + - - +
4026D LEU* 2.7 36.1 + - - +
4028D ALA* 1.3 82.4 + - - +
4030D ILE* 1.3 60.5 + - - +
4032D GLU* 2.9 44.1 + - - +
4033D ARG* 3.2 33.8 + - - +
305E G 2.7 37.8 + - - -
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Residues in contact with ILE4030 (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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4011D TYR* 4.2 35.0 - - + +
4014D THR* 4.1 22.7 - - + -
4015D ILE* 3.8 29.6 - - + -
4018D LEU* 4.7 4.7 - - + -
4026D LEU 3.8 7.4 - - - +
4027D ARG* 3.0 9.1 + - - +
4029D ARG* 1.3 73.0 - - - +
4031D ALA* 1.3 61.9 + - - +
4033D ARG 3.2 1.2 + - - -
4034D LEU* 2.8 57.5 + - + +
4041D VAL* 4.1 4.5 - - + -
4045D VAL* 4.6 6.1 - - + -
4062D LEU* 4.2 17.3 - - + -
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Residues in contact with ALA4031 (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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4027D ARG 2.9 11.7 + - - +
4028D ALA* 3.6 14.1 - - - +
4029D ARG 3.3 0.2 - - - -
4030D ILE* 1.3 76.0 - - - +
4032D GLU* 1.3 62.9 + - + +
4035D GLU* 3.0 20.6 + - - -
4036D GLN* 3.2 29.7 + - - +
4038D GLY* 4.6 11.4 - - - +
4041D VAL* 3.7 16.5 - - + +
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Residues in contact with GLU4032 (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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4028D ALA 3.2 9.3 + - - +
4029D ARG* 2.9 53.3 + - - +
4031D ALA* 1.3 82.1 - - - +
4033D ARG* 1.3 67.6 + - + +
4035D GLU* 3.5 13.0 + - - +
305E G 4.8 2.9 + - - -
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Residues in contact with ARG4033 (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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4014D THR* 4.1 23.7 + - + +
4017D GLU* 4.7 10.2 + - - +
4018D LEU* 3.0 36.4 - - - +
4021D GLU* 3.0 39.4 + - - +
4023D VAL* 4.9 5.9 - - - +
4029D ARG* 3.2 20.4 + - - +
4030D ILE 3.2 3.4 + - - +
4032D GLU* 1.3 77.7 + - + +
4034D LEU* 1.3 64.2 + - + +
4035D GLU* 3.1 16.0 + - - +
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Residues in contact with LEU4034 (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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4004D LEU* 4.3 22.2 - - + +
4010D MET* 4.0 25.1 - - + +
4011D TYR* 3.4 38.1 - - + -
4014D THR* 3.6 24.5 - - - +
4030D ILE* 2.8 28.6 + - + +
4033D ARG* 1.3 75.5 - - + +
4035D GLU* 1.3 70.4 + - - +
4036D GLN* 3.2 21.5 + - + +
4041D VAL* 6.3 0.4 - - + -
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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