Contacts of the strand formed by residues 1236 - 1240 (chain D) in PDB entry 6X34
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 THR1236 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839D LEU* 5.6 7.0 - - + +
1075D PHE* 5.7 6.2 - - - -
1076D ARG 4.3 6.1 - - - -
1077D ALA* 5.1 1.1 - - - +
1234D VAL 3.8 9.6 - - - +
1235D THR* 1.3 80.2 - - - +
1237D TRP* 1.3 70.3 + - - +
1238D PHE* 5.7 0.3 - - - -
1607D ARG* 4.3 0.5 - - - +
1608D MET* 3.4 39.6 + - - +
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Residues in contact with TRP1237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075D PHE* 3.3 7.6 - - - +
1076D ARG 2.9 41.0 + - - +
1077D ALA* 3.5 4.7 - - - +
1078D GLU* 3.4 45.0 - - + +
1235D THR* 4.2 9.9 + - - -
1236D THR* 1.3 82.3 + - - +
1238D PHE* 1.3 61.9 + - - +
1605D TRP* 4.7 24.2 - + + -
1606D SER* 3.4 29.2 - - - -
1607D ARG* 3.6 31.4 - - + -
1652D GLU* 4.5 19.5 - - + -
1653D LEU* 5.8 0.2 - - - -
1654D SER* 5.5 3.1 - - - -
1655D GLU* 3.9 33.4 - - + -
1656D ARG* 5.1 11.7 - - - -
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Residues in contact with PHE1238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695D TYR* 3.8 31.2 - + + -
829D TYR* 3.8 39.7 - + + -
1073D ARG* 4.3 7.9 - - - -
1074D ILE 3.9 4.9 - - - -
1075D PHE* 3.6 28.9 - + + -
1236D THR* 5.7 0.4 - - - +
1237D TRP* 1.3 75.6 - - - +
1239D SER* 1.3 73.2 + - - +
1240D LYS* 3.3 8.2 + - - -
1605D TRP* 4.3 4.3 - - - -
1606D SER* 3.1 45.9 + - - +
1607D ARG 3.3 25.8 - - - -
1608D MET* 4.0 14.4 - - + -
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Residues in contact with SER1239 (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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1072D VAL 4.3 2.5 + - - -
1073D ARG* 3.0 34.7 + - - +
1074D ILE* 2.9 39.1 + - - -
1111D PRO* 4.6 11.7 - - - -
1238D PHE* 1.3 71.9 - - - +
1240D LYS* 1.3 62.6 + - - +
1241D SER* 3.5 1.0 + - - -
1603D VAL* 3.7 20.8 - - - +
1604D SER 3.5 7.4 - - - -
1605D TRP* 5.0 4.9 - - - +
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Residues in contact with LYS1240 (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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695D TYR* 4.7 5.4 - - + -
1073D ARG* 4.5 0.7 - - - +
1238D PHE* 3.3 12.9 + - + -
1239D SER* 1.3 70.5 - - - +
1241D SER* 1.3 63.1 + - - +
1242D LEU* 3.4 14.1 + - + +
1244D GLN* 5.5 2.9 - - - +
1603D VAL* 3.3 6.1 - - - +
1604D SER* 2.9 38.8 + - - +
1605D TRP 4.5 1.1 - - - +
1606D SER* 3.7 26.0 - - - -
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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
------------------------------------------------------------
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