Contacts of the helix formed by residues 93 - 103 (chain P) in PDB entry 6P18
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 SER 93 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442 T 2.5 44.2 + - - -
452 T 3.4 24.2 - - - -
87P TYR* 4.4 3.4 - - - -
91P GLY 3.8 1.6 + - - -
92P SER* 1.3 77.8 - - - +
94P LYS* 1.3 65.6 + - - +
95P HIS 4.2 0.2 - - - -
96P ALA* 3.8 5.3 + - - +
97P ILE* 3.3 23.2 + - - +
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Residues in contact with LYS 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452 T 3.1 22.3 + - - +
462 G 3.3 25.0 + - - -
87P TYR* 3.6 29.8 - - + +
93P SER* 1.3 74.2 - - - +
95P HIS* 1.3 60.5 + - - +
97P ILE* 3.4 8.7 + - - +
98P ALA* 3.0 28.8 + - - +
130P VAL* 4.5 12.2 - - + +
131P ASP* 4.2 27.4 + - - +
134P LEU* 3.8 24.0 - - + -
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Residues in contact with HIS 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432 G 4.2 12.4 - - + +
442 T 3.2 56.8 - - + +
452 T 3.2 30.0 + - + +
93P SER 3.4 0.2 - - - -
94P LYS* 1.3 75.0 - - - +
96P ALA* 1.3 60.1 + - - +
98P ALA* 3.5 4.3 + - - +
99P SER* 2.9 36.1 + - - -
123P LEU* 4.2 25.3 - - + +
127P ARG* 4.3 14.7 - - - +
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Residues in contact with ALA 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442 T 3.4 24.8 + - - +
898C GLU* 4.7 15.9 - - + +
902C LEU* 4.6 5.4 - - + +
92P SER* 5.2 5.4 - - - -
93P SER* 3.8 12.3 + - - +
94P LYS 3.3 0.6 - - - -
95P HIS* 1.3 77.2 - - - +
97P ILE* 1.3 63.5 + - - +
99P SER* 3.8 6.1 - - - -
100P TYR* 3.1 24.6 + - - +
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Residues in contact with ILE 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902C LEU* 4.5 17.4 - - + +
906C PHE* 5.5 3.1 - - + -
83P ILE* 3.8 33.0 - - + +
86P SER* 3.8 19.3 - - - -
87P TYR* 3.9 20.6 - - + +
92P SER* 3.5 22.9 - - - +
93P SER 3.3 17.5 + - - +
94P LYS* 3.4 10.2 + - - +
95P HIS 3.4 0.2 - - - -
96P ALA* 1.3 77.0 - - - +
98P ALA* 1.3 57.5 + - - +
100P TYR* 3.5 2.4 + - - +
101P TYR* 3.0 28.6 + - + +
130P VAL* 3.8 17.3 - - + -
134P LEU* 6.3 1.1 - - + -
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Residues in contact with ALA 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P LYS 3.0 17.7 + - - +
95P HIS 3.9 3.8 - - - +
97P ILE* 1.3 74.0 - - - +
99P SER* 1.3 61.4 + - - +
101P TYR* 4.4 1.6 - - - -
102P HIS* 3.0 25.8 + - - +
123P LEU* 4.3 2.8 - - + +
126P CYS* 3.3 15.1 - - + +
127P ARG* 3.8 35.7 - - + +
130P VAL* 3.8 18.8 - - + -
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Residues in contact with SER 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95P HIS* 2.9 28.3 + - - -
96P ALA* 3.8 7.4 - - - -
97P ILE 3.3 0.2 - - - -
98P ALA* 1.3 77.9 - - - +
100P TYR* 1.3 57.3 + - - +
102P HIS* 3.4 3.1 + - - +
103P ARG* 3.0 41.7 + - - +
123P LEU* 4.0 18.0 - - - +
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Residues in contact with TYR 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895C LEU* 4.7 8.1 - - + +
899C GLU* 3.8 33.6 + - + -
902C LEU* 3.3 47.6 - - + -
903C ARG* 3.3 17.8 - - - +
906C PHE* 3.8 15.7 - + + -
907C GLY 3.1 20.3 + - - -
908C GLU* 4.7 1.0 + - - -
96P ALA 3.1 17.6 + - - +
97P ILE 4.0 1.6 - - - +
99P SER* 1.3 74.5 - - - +
101P TYR* 1.3 64.2 + - - +
103P ARG* 3.3 29.7 + - - +
104P VAL* 3.3 38.9 + - + +
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Residues in contact with TYR 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906C PHE* 3.5 43.7 - + + -
79P LYS* 4.9 11.7 - - + +
83P ILE* 5.1 6.5 - - + -
97P ILE* 3.0 19.9 + - + +
98P ALA* 4.4 1.6 - - - -
100P TYR* 1.3 75.8 - - - +
102P HIS* 1.3 64.2 + - - +
104P VAL* 4.7 4.0 - - + -
105P ALA* 3.2 42.3 + - + +
121P PRO* 6.0 2.5 - - + -
126P CYS* 3.6 15.7 - - - -
129P GLU* 3.2 34.7 + - + +
130P VAL* 6.1 2.5 - - + -
133P ILE* 5.6 6.0 - - + +
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Residues in contact with HIS 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P ALA 3.0 18.3 + - - +
99P SER* 3.7 3.4 - - - +
100P TYR 3.3 0.2 - - - -
101P TYR* 1.3 78.4 - - - +
103P ARG* 1.3 70.6 + - + +
104P VAL 3.2 1.3 + - - -
105P ALA* 4.3 2.1 + - - +
120P LYS* 3.2 33.9 + - + -
121P PRO* 2.9 34.0 + - - +
122P SER* 3.8 10.0 - - - -
123P LEU* 3.8 24.9 - - + -
126P CYS* 3.4 14.1 - - + -
51Q ARG* 4.0 40.3 + - + +
52Q VAL* 6.3 0.2 - - - -
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Residues in contact with ARG 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892C GLU* 4.2 27.3 + - - +
894C GLN 5.3 0.6 + - - -
895C LEU* 4.5 14.3 - - - +
899C GLU* 3.8 15.2 + - - -
909C LYS* 3.3 59.2 - - + +
99P SER* 3.0 30.3 + - - +
100P TYR* 3.3 39.8 + - - +
101P TYR 3.3 0.4 - - - -
102P HIS* 1.3 86.6 - - + +
104P VAL* 1.3 59.4 + - + +
120P LYS* 4.2 9.4 + - - +
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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