Contacts of the strand formed by residues 4067 - 4072 (chain D) in PDB entry 4O2W
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 LEU4067 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4015C ARG* 3.3 39.9 - - - +
4007D HIS 3.6 5.6 - - - +
4008D GLY 3.7 0.9 - - - +
4050D ALA 4.2 4.5 - - - +
4051D CYS* 3.6 7.6 - - - +
4052D GLY* 2.8 34.3 + - - -
4059D LEU* 3.7 19.7 - - + -
4061D GLN* 3.7 30.7 - - + +
4063D ASN* 5.6 1.6 - - - +
4065D ASP* 3.8 9.8 + - + +
4066D ASP* 1.3 79.3 - - - +
4068D HIS* 1.3 59.9 + - - +
4069D VAL 3.5 11.0 - - - +
4071D THR* 3.6 28.9 - - + +
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Residues in contact with HIS4068 (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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4005C GLY 3.5 25.5 + - - -
4006C ARG 5.0 2.2 + - - -
4008C GLY* 3.7 15.0 + - - -
4011C ALA* 2.9 35.2 + - - -
4012C GLU* 5.1 0.2 - - - -
4014C GLY 4.1 5.1 + - - -
4015C ARG* 3.7 23.3 + - + +
4068C HIS* 3.3 43.6 - + + -
4007D HIS 5.5 0.4 - - - +
4008D GLY* 4.2 11.4 - - - -
4011D ALA* 3.6 22.7 - - - +
4051D CYS* 4.6 0.4 - - - -
4066D ASP 4.3 1.0 + - - -
4067D LEU* 1.3 72.9 - - - +
4069D VAL* 1.3 72.7 + - + +
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Residues in contact with VAL4069 (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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4011C ALA 4.4 6.5 - - - +
4012C GLU* 4.6 15.5 - - + +
4014C GLY* 4.6 7.0 - - - -
4015C ARG* 3.8 27.4 - - + +
4011D ALA* 4.8 4.5 - - + -
4025D SER* 6.1 1.6 - - - -
4050D ALA 3.7 4.0 - - - +
4051D CYS* 3.9 7.2 - - - +
4067D LEU* 3.5 3.5 - - - +
4068D HIS* 1.3 103.2 - - + +
4070D LEU* 1.3 63.6 + - - +
4071D THR* 2.7 29.1 + - - +
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Residues in contact with LEU4070 (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 ALA* 5.2 1.6 - - - +
4025D SER* 3.9 20.9 + - - +
4026D PHE* 3.7 43.3 - - + -
4039D THR 4.3 2.7 - - - +
4041D VAL* 3.8 29.2 - - + -
4049D LEU* 4.0 23.1 - - + +
4050D ALA* 3.4 22.7 - - - +
4051D CYS* 3.8 21.2 - - - +
4069D VAL* 1.3 79.4 - - - +
4071D THR* 1.3 60.2 + - - +
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Residues in contact with THR4071 (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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4015C ARG* 4.0 20.2 - - - +
4049D LEU* 3.9 2.5 - - - -
4050D ALA 2.8 28.3 + - - +
4061D GLN* 3.5 24.8 + - - +
4067D LEU* 3.6 23.6 - - + +
4069D VAL* 2.7 22.3 + - - +
4070D LEU* 1.3 73.7 + - - +
4072D VAL* 1.3 70.5 + - - +
4073D ILE 3.5 0.5 + - - -
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Residues in contact with VAL4072 (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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4047D THR* 4.2 9.2 - - + -
4048D VAL 3.5 9.0 - - - +
4049D LEU* 3.9 21.5 - - + +
4061D GLN* 3.3 15.6 - - - +
4071D THR* 1.3 79.7 - - + +
4073D ILE* 1.3 70.9 + - - +
4074D SER* 3.3 14.3 + - - +
4077D GLN* 3.8 29.8 - - + +
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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