Contacts of the helix formed by residues 89 - 97 (chain P) in PDB entry 3FKS
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 89 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394O ASP* 4.8 6.4 + - - -
398O GLU* 4.9 6.4 + - - -
401O LYS* 4.3 17.0 + - - -
85P GLY 3.9 4.3 + - - -
86P SER* 3.2 28.3 - - - -
88P HIS* 1.3 79.8 - - - +
90P GLN* 1.3 68.3 + - - +
92P ALA* 3.4 5.4 + - - +
93P LYS* 3.3 29.7 + - - +
117P GLN* 4.9 7.9 - - - +
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Residues in contact with GLN 90 (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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86P SER* 3.1 35.4 + - - +
89P SER* 1.3 81.6 - - - +
91P LEU* 1.3 58.0 + - - +
93P LYS* 2.9 13.7 + - + +
94P ALA* 2.8 29.5 + - - +
175P PHE* 3.8 18.9 - - + +
177P PRO* 3.7 29.6 - - + +
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Residues in contact with LEU 91 (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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76P ALA* 5.2 0.7 - - + -
77P ILE 3.0 33.2 - - - +
78P THR* 3.4 10.5 - - + -
87P ILE 3.7 13.1 + - - +
89P SER 3.4 0.6 - - - -
90P GLN* 1.3 78.8 - - - +
92P ALA* 1.3 62.5 + - - +
93P LYS 3.2 0.5 + - - -
94P ALA* 3.3 6.6 + - + +
95P VAL* 3.2 25.9 + - + +
114P ILE* 4.1 9.9 - - + -
165P PHE* 3.9 18.2 - - + +
166P TYR 2.9 33.2 - - - +
167P ASN* 3.2 25.8 + - - +
177P PRO* 4.3 13.1 - - + +
178P SER 5.0 1.1 - - - +
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Residues in contact with ALA 92 (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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88P HIS 3.7 8.9 + - - +
89P SER 3.4 2.5 + - - +
90P GLN 3.3 0.4 - - - -
91P LEU* 1.3 77.1 - - - +
93P LYS* 1.3 58.3 + - - +
95P VAL* 3.5 10.6 - - - +
96P ARG* 3.1 26.3 + - - +
114P ILE* 3.5 24.6 - - + +
117P GLN* 3.3 34.9 - - + +
118P LEU* 3.9 10.8 - - + +
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Residues in contact with LYS 93 (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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398O GLU* 6.1 0.9 - - - -
89P SER* 3.3 19.9 + - - +
90P GLN* 2.9 14.5 + - + +
92P ALA* 1.3 78.3 - - - +
94P ALA* 1.3 62.1 + - - +
95P VAL 2.9 5.2 + - - -
96P ARG* 4.3 4.9 - - + +
97P ARG* 3.2 28.6 + - - +
117P GLN* 6.2 1.6 - - + -
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Residues in contact with ALA 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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90P GLN 2.8 14.9 + - - +
91P LEU* 3.3 13.9 + - + +
93P LYS* 1.3 71.6 - - - +
95P VAL* 1.3 62.4 + - - +
97P ARG* 3.1 36.3 + - - +
165P PHE* 4.2 23.6 - - + -
177P PRO* 3.9 26.5 - - + +
178P SER 5.3 0.2 - - - +
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Residues in contact with VAL 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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74P ILE* 5.2 4.5 - - + -
76P ALA* 4.7 13.9 - - + -
91P LEU* 3.2 16.3 + - + +
92P ALA* 3.5 13.0 - - - +
93P LYS 2.9 0.8 - - - -
94P ALA* 1.3 78.6 - - - +
96P ARG* 1.3 67.2 + - - +
97P ARG 2.9 11.6 + - - -
107P ILE* 4.2 20.2 - - + -
114P ILE* 5.7 0.4 - - + -
118P LEU* 3.8 27.1 - - + -
122P HIS* 5.6 1.8 - - + -
165P PHE* 4.1 35.1 - - + -
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Residues in contact with ARG 96 (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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92P ALA 3.1 14.7 + - - +
93P LYS* 3.5 5.8 + - + +
95P VAL* 1.3 79.4 - - - +
97P ARG* 1.3 60.0 + - - +
117P GLN 5.6 0.2 - - - +
118P LEU* 5.0 1.6 - - + -
121P THR* 4.4 13.0 - - + +
122P HIS* 3.6 39.7 + - + +
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Residues in contact with ARG 97 (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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93P LYS 3.2 14.4 + - - +
94P ALA* 3.1 42.7 + - - +
95P VAL 2.9 10.9 + - - -
96P ARG* 1.3 80.8 - - - +
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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