Contacts of the strand formed by residues 798 - 804 (chain C) in PDB entry 7KHE
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 GLN 798 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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692C THR* 4.1 4.9 - - - +
694C ARG* 2.9 31.3 + - - +
696C ASP* 3.9 20.8 - - + +
797C GLY* 1.3 79.8 - - - +
799C ASN* 1.3 62.3 + - - +
800C MET* 3.9 3.5 + - + +
827C ARG* 2.5 67.9 + - - +
828C PHE* 3.9 18.4 - - + -
1231C TYR* 3.5 8.5 - - - -
1232C MET* 2.9 33.1 + - - +
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Residues in contact with ASN 799 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696C ASP* 3.3 20.9 + - - +
697C LYS* 3.6 19.0 + - - +
699C LEU* 3.2 44.2 - - + +
798C GLN* 1.3 73.7 - - - +
800C MET* 1.3 63.1 + - - +
827C ARG* 4.0 13.7 + - - -
1229C TYR* 5.0 11.5 - - + -
1230C MET 3.4 12.3 - - - +
1231C TYR* 3.8 14.4 - - + +
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Residues in contact with MET 800 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798C GLN* 3.9 5.9 + - + +
799C ASN* 1.3 77.9 - - - +
801C ARG* 1.3 61.7 + - - +
802C VAL* 3.4 5.3 + - + +
818C VAL* 5.0 0.9 - - - -
822C VAL* 3.4 36.6 - - + -
827C ARG* 3.7 26.5 - - + +
828C PHE* 3.0 43.3 - - + -
1095C ASP* 4.3 10.3 - - + +
1096C ILE* 3.6 35.0 - - + -
1229C TYR* 3.3 5.9 - - - -
1230C MET 2.9 33.2 + - - +
1232C MET* 5.2 3.6 - - + +
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Residues in contact with ARG 801 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800C MET* 1.3 71.1 - - - +
802C VAL* 1.3 61.2 + - - +
1088C ASP* 3.9 23.2 + - - +
1092C THR* 2.4 46.3 + - - -
1093C PRO 4.3 12.4 + - - -
1094C VAL* 3.3 13.4 - - + +
1095C ASP* 3.1 24.4 + - - +
1096C ILE 2.9 23.9 + - - -
1119C MET* 4.2 17.1 - - - +
1210C ILE* 4.1 12.5 - - - +
1212C LEU* 6.0 0.4 - - - +
1227C VAL* 4.5 11.1 - - + +
1228C GLY* 4.3 6.0 - - - +
1229C TYR* 3.2 41.4 + - + -
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Residues in contact with VAL 802 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800C MET 3.7 11.2 - - - +
801C ARG* 1.3 76.7 - - - +
803C ALA* 1.3 59.7 + - - +
804C PHE* 4.3 14.8 - - + -
1094C VAL* 3.9 1.7 - - - +
1096C ILE* 3.3 24.2 - - + +
1098C LEU* 4.1 22.4 - - + -
1115C THR* 3.9 16.6 - - + -
1226C THR 4.0 0.3 - - - +
1227C VAL* 3.3 4.3 - - - +
1228C GLY 2.8 41.8 + - - +
1230C MET* 4.1 23.3 - - + -
1232C MET* 4.4 7.0 - - + -
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Residues in contact with ALA 803 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802C VAL* 1.3 74.8 - - - +
804C PHE* 1.3 61.2 - - - +
805C MET* 3.3 11.7 + - + -
1094C VAL* 3.7 22.4 - - + -
1096C ILE 2.9 7.1 + - - +
1097C VAL* 3.4 6.1 - - + +
1098C LEU* 2.9 24.0 + - - -
1212C LEU* 4.2 12.6 - - + -
1225C VAL* 4.7 3.4 - - + -
1226C THR 3.3 4.9 - - - +
1227C VAL* 3.7 17.7 - - + -
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Residues in contact with PHE 804 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802C VAL* 4.3 13.5 - - + -
803C ALA* 1.3 71.4 - - - +
805C MET* 1.3 62.1 + - - +
1072C ASN* 6.0 0.2 - - - -
1098C LEU* 3.4 38.8 - - + -
1099C ASN 4.4 11.4 - - - -
1100C PRO* 3.7 13.9 - - + -
1103C VAL* 4.4 18.2 - - + -
1111C GLN* 4.5 22.2 - - + -
1112C ILE* 4.8 11.0 - - + -
1115C THR* 3.7 25.4 - - + -
1225C VAL* 4.0 3.6 - - - +
1226C THR* 3.0 31.5 + - + +
1230C MET* 5.1 3.1 - - - -
638D SER* 2.8 37.8 - - - -
639D VAL* 4.9 6.1 - - + -
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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