Contacts of the helix formed by residues 94 - 102 (chain A) in PDB entry 1F6O
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 PRO 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLN* 1.3 86.7 - - + +
95A ALA* 1.3 67.3 - - - +
96A VAL 3.3 1.1 - - - +
97A PRO* 3.0 28.1 - - + +
98A LEU* 2.9 19.6 + - - +
173A GLN* 3.3 31.4 - - + +
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Residues in contact with ALA 95 (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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94A PRO* 1.3 70.6 - - - +
96A VAL* 1.3 58.1 + - - +
98A LEU* 3.6 1.0 - - - +
99A ALA* 2.8 33.3 + - - +
126A ALA* 3.7 12.5 - - + +
127A TYR 4.0 7.6 - - - +
128A LEU* 4.0 17.0 - - + +
172A SER* 3.2 25.7 + - - +
173A GLN 4.4 1.4 + - - -
177A ALA* 4.2 4.9 - - + +
178A CYS 3.9 18.4 - - - +
179A VAL* 3.7 2.8 - - - +
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Residues in contact with VAL 96 (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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94A PRO* 3.3 0.6 - - - +
95A ALA* 1.3 75.4 - - - +
97A PRO* 1.3 75.2 - - + +
99A ALA* 3.2 3.3 + - - +
100A ARG* 3.0 39.6 + - - +
126A ALA* 4.0 10.8 - - + -
128A LEU* 4.1 12.7 - - + +
275A LEU* 3.7 29.6 - - + -
277A PHE* 3.7 19.5 - - + -
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Residues in contact with PRO 97 (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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93A GLN* 4.2 15.0 - - + +
94A PRO* 3.0 39.7 - - + +
96A VAL* 1.3 95.2 - - + +
98A LEU* 1.3 55.6 + - - +
100A ARG* 3.3 8.4 + - + +
101A ALA* 2.8 32.5 + - - +
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Residues in contact with LEU 98 (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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90A PHE* 4.0 25.4 - - + +
91A PHE* 3.8 17.9 - - - +
93A GLN* 4.0 14.3 - - + +
94A PRO 2.9 18.4 + - - +
95A ALA 3.6 3.6 - - - +
97A PRO* 1.3 77.7 - - - +
99A ALA* 1.3 56.4 + - - +
101A ALA* 3.1 3.6 + - + +
102A PHE* 2.9 59.9 + - + -
170A ILE* 4.6 1.8 - - + +
171A SER 4.2 5.8 - - - +
172A SER* 3.5 29.4 - - - -
179A VAL* 3.6 15.9 - - + -
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Residues in contact with ALA 99 (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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95A ALA 2.8 22.2 + - - +
96A VAL 3.2 4.7 + - - +
98A LEU* 1.3 73.7 - - - +
100A ARG* 1.3 61.2 + - - +
102A PHE* 3.6 4.3 - - - +
103A LEU* 3.8 2.6 - - - +
124A THR* 2.8 38.6 + - - +
126A ALA* 4.1 9.0 - - + +
179A VAL* 3.7 25.1 - - + +
277A PHE* 3.9 17.5 - - + -
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Residues in contact with ARG 100 (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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96A VAL* 3.0 27.4 + - - +
97A PRO* 3.8 6.3 - - + +
99A ALA* 1.3 72.8 - - - +
101A ALA* 1.3 65.4 + - - +
102A PHE 3.1 1.8 - - - -
103A LEU* 3.2 32.6 + - + +
256A VAL* 3.7 35.0 + - + +
258A ALA* 4.4 10.1 - - - +
277A PHE* 3.3 44.9 - - + -
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Residues in contact with ALA 101 (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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90A PHE* 3.9 21.2 - - + -
93A GLN* 4.6 11.2 - - - +
97A PRO 2.8 19.5 + - - +
98A LEU* 3.1 7.6 + - - +
100A ARG* 1.3 75.9 - - - +
102A PHE* 1.3 64.9 + - - +
103A LEU 3.5 2.2 + - - +
105A GLN* 3.3 21.8 - - - +
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Residues in contact with PHE 102 (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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90A PHE* 3.4 31.4 - + - -
91A PHE* 3.7 26.7 - + - -
98A LEU* 2.9 24.3 + - + -
99A ALA 3.6 10.8 - - - +
100A ARG 3.1 0.2 - - - -
101A ALA* 1.3 77.9 - - - +
103A LEU* 1.3 65.1 + - - +
104A GLY 3.2 0.5 + - - -
105A GLN* 2.9 21.0 + - - +
121A ILE* 3.5 16.7 - - + +
124A THR* 3.9 8.5 - - + -
170A ILE* 3.9 29.2 - - + -
179A VAL* 3.5 39.7 - - + -
181A LEU* 4.0 11.9 - - + -
236A LEU* 5.2 0.2 - - + -
244A LEU* 3.7 13.5 - - + -
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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