Contacts of the helix formed by residues 993 - 999 (chain A) in PDB entry 6RQT
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 993 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966A LEU* 3.7 33.0 - - + -
968A SER* 3.0 22.5 + - - -
969A PHE* 3.4 40.9 - - + -
977A MET* 5.1 4.0 - - - +
991A LYS* 3.1 18.8 - - + +
992A PRO* 1.3 95.2 - - - +
994A GLU* 1.3 64.7 + - - +
995A TYR 3.4 2.2 - - - -
996A TYR* 3.5 9.9 + - - +
997A PHE* 3.3 27.2 + - + -
525B TRP* 5.1 0.9 - - + -
676B VAL* 3.3 18.1 - - + +
680B GLU* 5.7 4.2 - - - +
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Residues in contact with GLU 994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950A GLN* 3.0 29.3 + - - +
977A MET 4.8 0.2 - - - +
980A GLY* 4.3 3.8 - - - +
981A TYR 2.9 29.5 + - - +
982A VAL* 3.2 29.8 - - + +
983A LYS 4.7 0.7 - - - +
984A GLY 5.4 0.2 - - - +
986A PHE* 5.7 0.2 - - + -
990A ILE* 3.7 18.4 - - + -
991A LYS* 3.0 43.3 + - + +
993A GLN* 1.3 77.9 - - - +
995A TYR* 1.3 55.2 + - - +
997A PHE* 2.9 9.1 + - - +
998A HIS* 2.6 35.0 + - - +
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Residues in contact with TYR 995 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986A PHE* 5.6 1.3 - + - -
990A ILE* 3.5 12.7 - - + +
993A GLN 3.4 0.6 - - - -
994A GLU* 1.3 76.6 - - - +
996A TYR* 1.3 64.1 + - - +
997A PHE 3.4 0.2 + - - -
998A HIS* 4.2 7.9 - - + +
999A CYS* 3.3 38.3 + - - -
530B PRO* 5.2 2.7 - - + -
531B VAL* 3.6 12.5 - - + +
697B LEU* 3.7 32.5 - - + -
707B SER* 3.1 47.4 + - - -
708B ASP 5.5 0.2 - - - -
710B ASN 4.4 7.2 - - - -
712B SER* 4.9 3.4 - - - -
715B ASN* 2.6 40.1 + - - +
984B TRP* 3.4 28.6 - + + -
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Residues in contact with TYR 996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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966A LEU* 3.5 20.4 - - + -
993A GLN 3.5 9.4 + - - +
994A GLU 3.3 0.2 - - - -
995A TYR* 1.3 79.0 - - - +
997A PHE* 1.3 65.6 + + - +
998A HIS 3.6 0.2 - - - -
999A CYS* 3.8 7.5 + - - +
1000A MET* 3.8 15.9 + - + +
520B LEU* 3.6 18.9 - - + +
521B LEU 2.6 10.4 + - - -
522B PRO* 3.4 25.5 - - + +
524B SER* 2.5 39.8 + - - -
525B TRP* 3.6 23.8 - + + -
528B LEU 5.6 0.4 - - - -
530B PRO* 4.0 18.2 - - + -
696B ILE* 3.6 31.6 - - + -
984B TRP* 5.5 0.2 - - - -
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Residues in contact with PHE 997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950A GLN* 3.1 25.2 - - + +
957A VAL* 3.9 17.3 - - + -
965A THR* 3.2 35.9 - - - -
966A LEU* 3.7 22.7 - - + -
969A PHE* 4.2 17.7 - + - -
977A MET 5.9 1.6 - - - -
978A ALA* 5.4 0.4 - - - -
980A GLY* 4.3 28.9 - - - -
991A LYS* 6.6 0.2 - - - -
993A GLN* 3.3 16.5 + - + +
994A GLU* 2.9 15.0 + - - +
996A TYR* 1.3 88.4 - + - +
998A HIS* 1.3 61.8 + - - +
999A CYS 3.2 0.7 - - - -
1000A MET* 3.6 32.7 - - + +
1001A ALA 4.1 0.9 + - - -
522B PRO* 4.3 5.2 - - + -
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Residues in contact with HIS 998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A LEU* 3.5 14.4 - - + +
950A GLN* 3.1 39.5 + - + +
986A PHE* 3.4 20.4 - + + -
994A GLU 2.6 14.7 + - - +
995A TYR* 3.6 9.3 + - + +
996A TYR 3.6 0.2 - - - -
997A PHE* 1.3 73.8 - - - +
999A CYS* 1.3 58.5 + - - +
1000A MET 3.3 0.7 - - - -
1001A ALA* 3.8 7.2 + - + +
1002A GLY* 3.0 21.5 + - - -
711B GLN* 3.5 21.0 - - + +
712B SER* 3.0 35.5 + - - -
713B PRO* 3.6 14.6 - - + -
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Residues in contact with CYS 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995A TYR* 3.3 35.6 + - - +
996A TYR 3.9 4.9 - - - +
997A PHE 3.2 0.8 - - - -
998A HIS* 1.3 76.4 - - - +
1000A MET* 1.3 65.7 + - - +
1002A GLY 3.8 1.1 - - - +
1003A ARG* 3.4 20.8 + - - +
520B LEU* 3.7 18.6 - - + +
530B PRO* 3.3 35.7 - - + +
531B VAL* 4.7 1.6 - - - -
712B SER* 3.1 27.6 - - - +
716B MET* 5.2 0.2 - - + -
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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