Contacts of the strand formed by residues 93 - 97 (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 GLN 93 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84T PHE* 4.2 2.1 - - - -
92T CYS* 1.3 81.0 - - - +
94T ILE* 1.3 64.8 + - - +
95T VAL* 5.1 0.2 - - + -
115T SER* 4.7 0.2 - - - -
117T LYS* 3.6 14.2 - - + +
119T PHE* 3.9 17.1 - - + -
186T ASN 4.3 1.8 + - - -
187T MET* 3.4 23.5 - - - +
188T ASN* 2.7 53.4 - - - +
191T LEU* 3.8 18.4 - - + +
192T PRO 2.9 4.5 + - - +
193T THR* 3.2 24.6 + - + +
194T LEU* 2.9 24.6 + - - +
220T PHE* 4.0 1.2 - - - -
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Residues in contact with ILE 94 (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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81T ILE* 4.3 14.4 - - + -
84T PHE* 5.0 0.4 - - + -
85T LEU* 3.8 27.8 - - + -
92T CYS* 4.9 3.4 - - - -
93T GLN* 1.3 79.0 - - - +
95T VAL* 1.3 66.4 + - - +
96T ASN 4.5 0.2 - - - +
108T LEU* 4.2 18.8 - - + -
115T SER* 3.9 13.9 - - - +
117T LYS 3.3 6.3 + - - -
118T TYR* 3.7 25.0 - - + -
119T PHE* 2.8 30.1 + - - +
194T LEU* 3.2 21.8 - - + +
196T ILE* 3.8 25.4 - - + -
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Residues in contact with VAL 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93T GLN* 5.1 0.4 - - + -
94T ILE* 1.3 79.0 - - - +
96T ASN* 1.3 59.8 + - - +
97T LEU* 3.4 26.1 + - + +
119T PHE* 3.4 28.3 - - + -
121T VAL* 4.2 5.6 - - + -
182T LEU* 4.0 18.2 - - + -
187T MET* 4.4 14.1 - - - -
193T THR* 3.8 23.3 - - + -
194T LEU 2.8 9.3 + - - -
195T LEU* 3.3 17.4 - - + -
196T ILE 3.0 23.0 + - - -
215T TRP* 6.1 0.2 - - + -
220T PHE* 5.2 0.2 - - + -
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Residues in contact with ASN 96 (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 4.6 5.5 + - - -
94T ILE* 3.9 2.2 - - - +
95T VAL* 1.3 70.0 - - - +
97T LEU* 1.3 68.2 + - - +
98T GLY 4.3 0.7 - - - +
99T ALA* 3.5 28.0 + - + +
102T ASP* 3.2 36.0 + - - +
104T THR* 5.0 0.2 + - - -
118T TYR* 3.6 17.6 + - + +
119T PHE 2.8 12.5 + - - +
120T GLU* 3.6 2.9 - - + -
121T VAL* 3.0 27.5 + - - +
196T ILE* 3.4 30.8 - - + +
198T GLU* 5.0 3.3 + - - +
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Residues in contact with LEU 97 (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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95T VAL* 3.8 29.6 - - + +
96T ASN* 1.3 71.4 - - - +
98T GLY* 1.3 65.6 + - - +
121T VAL* 4.2 9.4 - - + -
172T LEU* 3.8 28.3 - - + -
178T LEU* 4.8 10.3 - - + -
182T LEU* 5.8 0.2 - - + -
195T LEU* 3.9 26.0 - - + -
196T ILE 2.6 21.7 + - - +
197T ALA* 3.9 7.0 - - + -
198T GLU 4.4 0.7 + - - -
200T VAL* 3.4 14.6 - - + +
212T LEU* 4.4 18.4 - - + -
215T TRP* 5.4 1.1 - - + -
225T PHE* 4.0 26.7 - - + -
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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