Contacts of the strand formed by residues 92 - 96 (chain F) in PDB entry 6AHU
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 HIS 92 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90F GLY 3.6 1.2 - - - -
91F LEU* 1.3 99.1 + - + +
93F GLN* 1.3 62.4 - - - +
138F LEU 3.6 0.6 - - - +
139F LEU* 3.6 5.0 - - - +
140F SER 2.9 38.6 + - - +
141F LYS* 3.8 23.8 + - + -
144F LEU* 3.8 39.7 + - + +
148F GLN* 4.8 8.3 - - - -
153F PRO* 3.4 26.1 + - + +
154F PRO 4.0 0.9 - - - -
155F ASN* 5.1 9.2 - - + -
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Residues in contact with GLN 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F ALA* 4.9 5.5 - - - +
82F GLU* 5.4 1.2 + - - -
85F LYS* 6.0 8.4 - - - +
92F HIS* 1.3 75.0 - - - +
94F VAL* 1.3 62.9 + - - +
95F THR* 3.9 8.5 + - - +
137F ILE* 3.6 26.1 - - + +
138F LEU 3.4 4.9 - - - -
139F LEU* 3.6 23.3 - - + +
153F PRO* 3.3 22.1 - - - +
154F PRO* 3.5 33.1 + - + +
156F PRO* 6.3 0.4 - - - +
100G ALA 5.2 1.2 - - - +
102G THR* 2.6 35.7 + - - +
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Residues in contact with VAL 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F PHE* 6.2 1.1 - - + -
93F GLN* 1.3 73.7 - - - +
95F THR* 1.3 62.4 + - - +
96F ARG* 3.7 38.7 + - + +
136F ALA 3.0 13.5 - - - +
138F LEU* 3.1 39.3 + - + +
144F LEU* 3.8 30.3 - - + -
147F ARG* 5.8 2.2 - - - +
151F TYR* 5.2 24.7 - - + +
153F PRO* 4.8 4.0 - - + -
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Residues in contact with THR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F GLN* 3.9 9.6 + - - +
94F VAL* 1.3 73.3 - - - +
96F ARG* 1.3 60.6 + - - +
97F LEU* 3.7 13.0 - - + +
135F LEU* 3.8 36.6 - - + -
136F ALA 3.3 4.0 - - - +
137F ILE* 3.8 15.8 - - + +
98G VAL 4.7 6.1 - - - +
99G ALA* 5.0 0.7 - - - -
100G ALA* 3.7 45.1 + - + -
102G THR* 4.6 11.3 + - + +
130G ILE* 4.7 2.5 - - + -
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Residues in contact with ARG 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F GLY* 3.4 37.5 - - - +
22F GLY 4.2 1.2 - - - +
23F PRO* 4.7 2.9 - - - +
24F GLY* 3.4 39.3 - - - +
28F PHE* 5.4 3.0 - - - -
94F VAL* 3.7 27.5 - - + +
95F THR* 1.3 77.8 - - - +
97F LEU* 1.3 61.7 + - - +
98F ARG* 4.1 15.3 + - + +
135F LEU* 3.5 8.1 + - - +
136F ALA* 3.2 33.5 + - + +
138F LEU* 4.6 15.3 - - + +
147F ARG* 5.9 1.6 - - - +
151F TYR* 5.1 17.2 + - - -
98G VAL 5.8 1.3 - - - -
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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