Contacts of the strand formed by residues 117 - 122 (chain T) in PDB entry 3P71
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 LYS 117 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92T CYS 3.6 3.0 + - - -
93T GLN* 3.6 10.0 - - + +
94T ILE 3.3 17.3 + - - +
115T SER* 3.2 13.8 + - - -
116T SER* 1.3 82.2 - - - +
118T TYR* 1.3 64.2 + - - +
119T PHE* 3.6 35.2 - - + -
161T ASP* 3.0 14.5 + - - -
162T SER 2.7 28.9 + - - -
163T LYS* 3.2 14.7 + - - +
164T ARG 3.3 11.9 - - - +
165T TYR 4.1 1.3 - - - +
166T ALA* 4.1 9.0 - - - -
185T CYS 2.9 24.9 + - - +
186T ASN* 5.0 8.4 - - - +
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Residues in contact with TYR 118 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81T ILE* 6.3 0.4 - - + -
94T ILE* 3.7 33.3 - - + +
96T ASN* 3.6 17.6 + - + +
102T ASP* 2.9 20.2 + - - -
104T THR* 3.5 16.2 + - + +
105T PHE* 3.8 24.5 - + + -
108T LEU* 4.1 27.8 - - + -
114T LEU* 5.5 2.5 - - + -
115T SER* 4.5 4.0 - - - +
117T LYS* 1.3 74.5 - - - +
119T PHE* 1.3 66.7 + - - +
120T GLU* 3.4 29.4 - - + -
164T ARG 2.7 15.2 + - - +
165T TYR* 3.3 20.0 - + + -
166T ALA* 2.8 26.5 + - - +
196T ILE* 4.8 3.6 - - - +
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Residues in contact with PHE 119 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93T GLN* 3.9 21.1 - - + -
94T ILE 2.8 20.5 + - - +
95T VAL* 3.4 25.0 - - + -
96T ASN* 2.8 27.5 + - - +
117T LYS* 3.6 42.0 - - + -
118T TYR* 1.3 75.8 - - - +
120T GLU* 1.3 64.8 + - - +
166T ALA* 3.6 14.8 - - + -
168T ILE* 4.3 6.1 - - + -
182T LEU* 3.8 21.3 - - + -
185T CYS* 3.6 26.7 - - + -
186T ASN 4.4 0.2 - - - -
187T MET* 3.6 31.2 - - + -
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Residues in contact with GLU 120 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96T ASN* 3.6 3.4 - - + -
99T ALA* 3.6 16.1 - - + +
102T ASP* 3.0 31.4 - - - +
104T THR 5.2 0.2 + - - -
105T PHE* 5.5 0.7 + - - +
118T TYR* 3.4 25.4 - - + -
119T PHE* 1.3 72.7 - - - +
121T VAL* 1.3 63.8 + - - +
130T LYS* 2.7 37.3 + - - +
165T TYR* 2.8 21.3 + - + -
166T ALA 2.8 13.8 + - - +
167T VAL* 3.6 11.4 - - + +
168T ILE* 2.7 32.6 + - - +
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Residues in contact with VAL 121 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310C AN6 5.2 0.2 - - - -
95T VAL* 4.2 12.1 - - + -
96T ASN 3.0 12.7 + - - +
97T LEU* 4.2 16.2 - - + -
98T GLY 2.9 23.6 + - - -
99T ALA* 3.0 10.3 + - - +
120T GLU* 1.3 80.7 - - - +
122T ASP* 1.3 63.4 - - - +
127T VAL* 5.1 0.4 - - - -
168T ILE* 3.3 15.0 - - + +
170T ALA* 4.3 17.0 - - + +
172T LEU* 4.0 14.1 - - + -
178T LEU* 3.7 31.6 - - + -
182T LEU* 4.4 10.8 - - + -
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Residues in contact with ASP 122 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C AN6 2.7 50.0 + - - -
98T GLY 3.2 2.3 - - - -
99T ALA* 3.2 8.7 + - + +
100T GLY 2.8 28.9 + - - +
121T VAL* 1.3 73.4 - - - +
123T PHE* 1.3 68.8 + - - +
126T ILE* 3.4 25.6 - - + +
127T VAL* 4.0 9.2 - - + +
168T ILE 3.1 5.1 + - - -
169T GLY* 3.2 4.9 - - - -
170T ALA 2.8 32.7 + - - -
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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