Contacts of the strand formed by residues 96 - 101 (chain A) in PDB entry 3P11
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 PHE 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A TYR* 3.7 1.4 - - - +
91A VAL* 2.9 17.2 - - - +
92A TYR* 3.1 30.6 + - + +
93A ASP* 4.0 18.2 - - + -
95A LYS* 1.3 87.2 - - + +
97A ALA* 1.3 62.5 + - - +
98A ILE* 3.3 12.0 - - - +
99A PHE* 3.9 28.9 - + + -
127A GLY 3.9 1.6 - - - -
128A VAL 3.8 13.9 - - - -
129A TYR* 3.6 32.3 - + + -
154A GLU* 3.7 42.0 - - + -
156A VAL* 4.7 5.8 - - + -
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Residues in contact with ALA 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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67A TYR* 3.3 12.8 - - - -
68A VAL 2.8 23.9 + - - -
86A VAL* 3.9 11.5 - - + +
88A GLY* 4.5 2.9 - - - -
91A VAL* 3.4 5.3 - - - +
96A PHE* 1.3 72.8 - - - +
98A ILE* 1.3 62.5 + - - +
123A ILE* 3.3 24.9 - - + -
125A SER 3.3 25.8 - - - +
126A GLY* 4.1 0.7 - - - -
127A GLY 3.0 13.0 + - - +
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Residues in contact with ILE 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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68A VAL* 3.5 24.0 - - + +
83A LEU* 6.4 1.3 - - + -
86A VAL* 5.1 7.0 - - + -
96A PHE* 3.9 3.9 - - - +
97A ALA* 1.3 85.1 - - - +
99A PHE* 1.3 62.7 + - - +
100A VAL* 3.9 22.2 - - + -
115A LEU* 6.2 1.1 - - + -
117A LEU* 5.4 7.0 - - + -
120A LEU* 4.2 17.7 - - + -
123A ILE* 3.3 29.2 - - + -
127A GLY 3.4 2.6 + - - -
128A VAL* 3.3 19.9 - - + -
129A TYR 2.8 26.0 + - - -
130A ILE* 5.1 2.2 - - + -
144A TRP* 4.2 13.0 - - + -
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Residues in contact with PHE 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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17A LEU* 5.8 3.6 - - + -
67A TYR* 6.1 0.2 - - + -
68A VAL 3.1 8.3 + - - +
69A LEU* 3.6 21.0 - - + +
70A VAL 2.9 26.9 + - - +
92A TYR* 3.3 48.5 - + + -
93A ASP* 4.1 9.9 - - - -
96A PHE* 3.9 23.1 - + + +
98A ILE* 1.3 74.2 - - - +
100A VAL* 1.3 60.6 + - - +
101A MET* 3.6 34.5 - - + -
129A TYR* 3.5 37.7 - + + -
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Residues in contact with VAL 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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70A VAL* 3.4 20.9 - - + -
98A ILE* 3.9 20.0 - - + -
99A PHE* 1.3 75.5 - - - +
101A MET* 1.3 56.5 + - - +
103A ASN* 3.8 12.3 - - - +
112A LEU* 4.3 9.2 - - + -
115A LEU* 4.4 17.5 - - + -
129A TYR 2.6 14.7 + - - +
130A ILE* 4.1 8.5 - - + -
131A GLU 3.1 15.1 + - - -
133A ASN* 2.7 40.8 + - - +
136A LEU* 4.2 13.0 - - + -
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Residues in contact with MET 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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17A LEU* 6.6 0.4 - - - -
70A VAL 3.2 7.1 + - - +
71A ALA* 3.4 22.9 - - + +
72A MET* 3.6 0.7 + - - +
99A PHE* 3.6 35.8 + - + -
100A VAL* 1.3 75.6 - - - +
102A LEU* 1.3 100.0 + - + +
103A ASN* 3.6 0.4 - - - -
129A TYR* 3.7 24.7 - - + +
131A GLU 3.3 7.0 - - - +
132A LYS* 3.8 26.0 - - + +
133A ASN* 3.4 2.5 - - - -
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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