Contacts of the helix formed by residues 1101 - 1109 (chain K) in PDB entry 6R90
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 SER1101 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1099K ASP 4.2 0.4 + - - -
1100K ILE* 1.3 80.3 - - - +
1102K ARG* 1.3 59.2 + - - +
1103K PRO* 3.5 13.4 - - - +
1104K LYS* 3.2 28.4 + - - +
1105K MET* 2.8 24.8 + - - +
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Residues in contact with ARG1102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100K ILE 3.8 0.6 + - - -
1101K SER* 1.3 73.3 - - - +
1103K PRO* 1.3 70.5 - - + +
1105K MET* 3.1 17.2 + - + +
1106K GLN* 2.9 45.2 + - + +
1125K THR* 5.4 0.8 - - - +
1126K ALA* 4.5 3.3 - - + +
1127K ASP* 3.0 39.4 + - - -
1130K ILE* 3.9 17.8 - - - +
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Residues in contact with PRO1103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101K SER* 3.5 15.0 - - - +
1102K ARG* 1.3 92.9 - - + +
1104K LYS* 1.3 57.9 + - + +
1106K GLN* 3.2 12.2 + - + +
1107K GLU* 2.9 35.4 + - - +
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Residues in contact with LYS1104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061K VAL* 4.2 17.3 - - + +
1063K LYS* 6.3 2.9 - - - +
1100K ILE* 3.5 28.9 - - + -
1101K SER* 3.2 17.1 + - - +
1103K PRO* 1.3 76.2 - - + +
1105K MET* 1.3 60.3 + - - +
1107K GLU* 3.3 30.0 + - - +
1108K VAL* 2.9 33.3 + - - +
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Residues in contact with MET1105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097K PHE* 3.0 58.5 - - + +
1098K LEU* 3.6 20.4 - - - +
1100K ILE* 3.3 19.5 - - + +
1101K SER 2.8 15.9 + - - +
1102K ARG* 3.1 20.4 + - - +
1104K LYS* 1.3 76.4 - - - +
1106K GLN* 1.3 60.9 + - - +
1108K VAL* 3.1 15.1 + - - +
1109K VAL* 3.2 17.3 + - - +
1126K ALA* 4.1 9.2 - - + -
1130K ILE* 3.8 28.7 - - + -
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Residues in contact with GLN1106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102K ARG* 2.9 33.7 + - + +
1103K PRO* 3.4 11.4 - - + +
1105K MET* 1.3 72.2 - - - +
1107K GLU* 1.3 61.4 + - - +
1109K VAL* 3.3 13.1 + - - +
1110K ALA* 2.9 28.2 + - - +
1124K ALA 5.6 0.2 - - - +
1125K THR* 3.8 14.6 - - - +
1126K ALA* 3.1 33.2 + - + +
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Residues in contact with GLU1107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057K ARG* 4.9 0.9 + - - +
1061K VAL* 4.8 14.5 - - + +
1103K PRO* 2.9 21.2 + - - +
1104K LYS* 3.3 43.7 + - - +
1106K GLN* 1.3 77.5 - - - +
1108K VAL* 1.3 62.1 + - - +
1110K ALA* 3.2 22.1 + - - +
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Residues in contact with VAL1108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054K MET* 5.0 8.5 - - + +
1057K ARG* 3.4 42.8 + - + +
1058K LEU* 3.8 42.2 - - + -
1061K VAL* 3.8 26.0 - - + -
1097K PHE* 4.2 13.7 - - + -
1100K ILE* 6.0 1.8 - - + -
1104K LYS 2.9 20.6 + - - +
1105K MET* 3.1 10.0 + - - +
1107K GLU* 1.3 76.2 - - - +
1109K VAL* 1.3 62.8 + - + +
1112K LEU* 4.5 1.6 - - + +
1129K LEU* 6.0 0.7 - - + -
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Residues in contact with VAL1109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097K PHE* 4.8 2.0 - - + -
1105K MET 3.2 13.6 + - - +
1106K GLN* 3.5 20.4 - - - +
1108K VAL* 1.3 82.1 - - + +
1110K ALA* 1.3 64.7 + - - +
1112K LEU* 3.3 20.8 - - + +
1123K GLU* 3.2 19.1 - - - +
1124K ALA 3.5 21.0 - - - +
1125K THR* 4.2 3.1 - - - +
1126K ALA* 3.7 18.4 - - - +
1129K LEU* 3.7 37.0 - - + -
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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
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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