Contacts of the helix formed by residues 1112 - 1122 (chain A) in PDB entry 6DMY
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 ASN1112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744A LEU* 4.9 4.6 - - + +
745A LEU* 4.6 18.7 - - + +
747A PRO* 4.8 16.4 + - - +
748A LYS* 5.7 5.1 - - - +
1104A PHE* 5.8 0.9 - - - -
1111A LYS* 1.3 75.4 - - - +
1113A ARG* 1.3 66.5 + - - +
1114A ARG 3.1 2.1 + - - -
1115A ALA* 3.4 12.9 + - - +
1116A VAL* 3.3 16.7 + - - +
1176A SER* 3.8 40.8 + - - +
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Residues in contact with ARG1113 (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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738A LYS* 3.6 14.8 - - - +
745A LEU* 5.5 5.9 - - - +
1109A GLY* 5.1 11.0 - - - -
1111A LYS* 3.0 11.4 - - + +
1112A ASN* 1.3 83.4 + - - +
1114A ARG* 1.3 61.8 + - - +
1116A VAL* 3.3 47.9 + - - +
1117A LEU* 3.5 15.5 + - - +
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Residues in contact with ARG1114 (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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1104A PHE* 3.3 43.4 - - + +
1107A ALA* 3.7 30.1 + - + +
1108A ILE 4.2 0.6 + - - -
1109A GLY* 2.6 36.9 + - - +
1110A ASP* 3.3 30.2 + - - +
1111A LYS 2.9 13.0 + - - +
1113A ARG* 1.3 78.2 - - - +
1115A ALA* 1.3 57.7 + - - +
1116A VAL 3.2 0.5 + - - -
1117A LEU* 3.4 3.2 + - - +
1118A ALA* 2.9 26.3 + - - +
1180A PRO* 4.2 6.5 - - - +
1181A TYR 3.9 3.6 - - - +
1182A PRO* 2.1 61.6 - - - +
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Residues in contact with ALA1115 (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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744A LEU* 5.0 4.3 - - + +
1104A PHE* 3.5 26.1 - - + -
1112A ASN 3.4 6.2 + - - +
1114A ARG* 1.3 76.2 - - - +
1116A VAL* 1.3 59.0 + - - +
1118A ALA* 3.9 4.0 - - - +
1119A LEU* 2.9 31.6 + - - +
1172A PRO* 3.9 20.0 - - + +
1176A SER* 3.4 26.2 - - - +
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Residues in contact with VAL1116 (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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738A LYS* 3.6 17.7 - - - +
741A ALA* 3.7 22.9 - - + +
744A LEU* 4.7 8.5 - - + -
745A LEU* 4.4 26.5 - - + -
1112A ASN 3.3 17.5 - - - +
1113A ARG* 3.3 42.0 - - - +
1114A ARG 3.1 0.8 - - - -
1115A ALA* 1.3 76.9 - - - +
1117A LEU* 1.3 59.8 + - + +
1119A LEU* 3.2 5.0 + - - +
1120A GLU* 2.9 26.8 + - + +
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Residues in contact with LEU1117 (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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1107A ALA* 4.9 15.0 - - + -
1113A ARG* 3.5 12.9 + - - +
1114A ARG* 3.4 6.0 + - - +
1116A VAL* 1.3 79.0 - - + +
1118A ALA* 1.3 61.5 + - - +
1120A GLU* 3.4 28.0 - - + +
1121A HIS* 2.9 52.6 + - + +
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Residues in contact with ALA1118 (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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1100A VAL* 4.6 8.2 - - - +
1103A ALA* 3.4 50.3 - - + +
1104A PHE* 3.6 13.9 - - + +
1107A ALA* 4.9 1.7 - - - +
1114A ARG 2.9 17.7 + - - +
1115A ALA* 3.9 8.7 - - - -
1117A LEU* 1.3 76.9 - - - +
1119A LEU* 1.3 61.8 + - - +
1120A GLU 3.4 0.2 + - - -
1121A HIS* 3.5 6.9 + - - -
1122A MET* 3.9 6.9 + - - +
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Residues in contact with LEU1119 (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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737A GLU* 4.4 8.1 - - + +
740A TYR* 3.5 39.7 - - + -
741A ALA* 4.0 24.2 - - + +
744A LEU* 5.3 6.3 - - + -
1100A VAL* 5.4 10.5 - - + +
1115A ALA 2.9 21.1 + - - +
1116A VAL* 3.6 2.5 - - - +
1118A ALA* 1.3 77.2 - - - +
1120A GLU* 1.3 59.7 + - - +
1122A MET 4.7 0.3 - - - -
1123A PHE* 3.3 33.4 + - + +
1168A LEU* 4.1 10.1 - - + +
1172A PRO* 3.7 34.1 - - + +
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Residues in contact with GLU1120 (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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520A HIS* 5.8 0.3 + - - -
524A GLU* 5.7 1.0 - - - +
734A SER* 3.6 29.7 - - - +
737A GLU* 3.7 30.5 - - + +
738A LYS* 5.2 9.6 - - - +
741A ALA* 5.8 0.7 - - + -
1116A VAL* 2.9 16.7 + - + +
1117A LEU* 3.4 27.6 - - + +
1118A ALA 3.2 0.2 - - - -
1119A LEU* 1.3 79.4 - - - +
1121A HIS* 1.3 68.2 + - - +
1122A MET 3.3 2.1 + - - -
1123A PHE* 3.8 8.8 + - - +
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Residues in contact with HIS1121 (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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520A HIS* 3.5 24.8 + + - -
524A GLU* 5.4 8.1 - - - -
543A ARG* 3.5 26.8 + - - -
1103A ALA* 4.5 10.0 + - + +
1106A THR* 5.0 9.2 + - - -
1117A LEU* 2.9 34.7 + - + +
1118A ALA* 4.0 7.0 - - - +
1119A LEU 3.5 0.6 - - - -
1120A GLU* 1.3 84.9 - - - +
1122A MET* 1.3 75.6 + - + +
1123A PHE 3.8 0.4 - - - -
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Residues in contact with MET1122 (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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517A LEU* 4.6 19.7 - - - -
520A HIS* 5.3 3.4 - - + -
543A ARG 5.8 2.0 - - - +
544A THR* 5.5 11.4 - - + -
547A SER* 6.4 1.8 - - - -
1099A HIS* 3.9 33.2 - - + +
1100A VAL* 4.8 7.2 - - + -
1102A LEU* 4.4 23.3 - - + -
1103A ALA* 3.7 24.7 - - + -
1118A ALA 3.9 7.8 + - - +
1119A LEU 4.7 0.2 - - - -
1120A GLU 3.3 0.2 - - - -
1121A HIS* 1.3 96.0 - - + +
1123A PHE* 1.3 65.6 + - - +
1124A ALA 3.6 1.3 - - - -
1125A PRO* 3.4 16.5 - - - +
1126A VAL* 3.3 18.4 - - + +
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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