Contacts of the strand formed by residues 4133 - 4139 (chain D) in PDB entry 2H7C
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 LEU4133 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4124D PRO* 3.9 18.4 - - + -
4125D ALA* 3.6 29.4 - - + -
4131D ASN* 4.2 14.4 - - + +
4132D ARG* 1.3 78.2 - - - +
4134D PRO* 1.3 80.2 - - + +
4135D VAL 3.4 0.2 + - - -
4162D ASN* 3.4 46.7 - - - +
4164D VAL* 4.2 8.7 - - + +
4209D GLY 3.0 14.4 + - - +
4210D GLY* 3.4 2.8 - - - -
4211D ASN* 2.8 27.8 + - - +
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Residues in contact with PRO4134 (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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4132D ARG 4.0 2.7 - - - +
4133D LEU* 1.3 89.5 - - + +
4135D VAL* 1.3 58.7 + - - +
4136D MET* 5.3 0.2 - - - -
4162D ASN 4.1 5.8 - - - +
4163D VAL* 3.5 26.9 - - + +
4164D VAL* 2.9 24.1 + - - -
4214D SER* 3.7 24.2 - - - +
4504D ALA* 4.4 14.8 - - + +
4505D ARG* 3.7 28.7 - - + +
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Residues in contact with VAL4135 (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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4133D LEU 3.6 9.4 - - - +
4134D PRO* 1.3 77.5 - - - +
4136D MET* 1.3 60.4 + - - +
4137D VAL* 4.1 13.5 - - + -
4164D VAL* 3.4 13.2 - - + +
4166D VAL* 3.9 22.9 - - + -
4201D VAL* 4.3 5.4 - - + -
4205D ILE* 3.7 29.8 - - + -
4210D GLY* 3.9 3.6 - - - -
4211D ASN 3.8 19.5 - - - +
4214D SER 3.0 9.6 + - - +
4215D VAL* 3.5 8.4 - - + -
4216D THR* 2.7 35.7 + - - -
4504D ALA* 5.1 0.2 - - - +
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Residues in contact with MET4136 (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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4135D VAL* 1.3 77.2 - - - +
4137D VAL* 1.3 62.5 + - - +
4138D TRP 3.8 0.5 + - - -
4157D LEU* 4.4 11.0 - - + -
4163D VAL* 4.0 27.1 - - + -
4164D VAL 2.8 12.0 + - - +
4165D VAL* 3.5 8.1 - - + +
4166D VAL 2.9 26.2 + - - +
4216D THR* 3.3 16.4 - - + +
4218D PHE* 3.7 36.0 - - + -
4244D ILE* 4.6 2.0 - - + -
4500D TRP* 3.8 33.4 - - + +
4501D ALA* 4.3 11.2 - - - -
4504D ALA* 3.9 24.0 - - + -
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Residues in contact with VAL4137 (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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4135D VAL* 4.1 12.6 - - + -
4136D MET* 1.3 73.5 - - - +
4138D TRP* 1.3 61.8 + - - +
4139D ILE* 4.4 3.0 - - + +
4166D VAL* 3.3 13.0 - - + +
4168D ILE* 3.7 36.3 - - + -
4197D ALA* 5.9 0.2 - - + -
4198D LEU* 4.1 23.6 - - + -
4201D VAL* 4.3 11.2 - - + -
4215D VAL* 3.8 25.4 - - + -
4216D THR 2.8 12.0 + - - +
4217D ILE* 3.4 6.6 - - + +
4218D PHE* 3.0 28.2 + - - +
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Residues in contact with TRP4138 (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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4137D VAL* 1.3 72.6 - - - +
4139D ILE* 1.3 67.0 + - - +
4140D HIS* 3.6 14.1 + - + +
4141D GLY 5.2 0.2 - - - -
4149D ALA* 5.6 1.1 - - - -
4152D TYR* 3.5 42.5 - + - -
4165D VAL* 5.3 0.9 - - + -
4166D VAL 2.7 15.0 + - - +
4167D THR* 4.1 18.2 - - + -
4168D ILE* 3.3 28.6 + - - +
4218D PHE* 3.3 58.2 - + + -
4219D GLY* 3.5 12.6 - - - -
4220D GLU* 3.5 24.2 - - + -
4246D GLU* 3.8 9.2 - - - -
4472D LEU* 3.3 35.2 - - + -
4475D VAL* 5.2 0.7 - - + -
4476D PHE* 3.4 24.9 - + + -
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Residues in contact with ILE4139 (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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4137D VAL* 4.4 7.0 - - + +
4138D TRP* 1.3 79.0 - - - +
4140D HIS* 1.3 63.3 + - - +
4168D ILE* 4.0 19.7 - - + -
4170D TYR* 3.8 14.1 - - + -
4194D GLN* 3.6 29.2 - - + +
4198D LEU* 5.7 1.3 - - + -
4217D ILE* 4.8 7.6 - - + -
4218D PHE 2.9 15.2 + - - +
4219D GLY* 3.1 19.9 - - - -
4220D GLU 3.6 1.7 + - - -
4223D GLY* 3.2 20.8 - - - +
4226D SER* 4.0 6.7 - - - +
4227D VAL* 4.1 17.9 - - + -
4230D LEU* 3.9 28.3 - - + -
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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