Contacts of the strand formed by residues 77 - 83 (chain B) in PDB entry 2P2L
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 VAL 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.0 6.7 - - + -
5B LYS 3.2 2.4 + - - +
6B CYS* 3.2 32.4 - - + -
7B VAL 3.1 21.7 + - - -
75B THR* 3.3 8.7 - - - +
76B ASP* 1.3 82.1 - - - +
78B SER* 1.3 72.1 + - - +
79B LEU* 5.0 0.7 - - + -
108B THR* 5.1 1.1 - - - -
109B PRO* 3.5 24.2 - - + +
111B ILE* 4.5 7.2 - - + -
172B ALA* 3.9 32.1 - - + +
175B ALA* 4.4 7.2 - - + -
176B VAL* 3.8 12.3 - - + -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL 3.2 9.9 - - - -
9B VAL* 5.2 1.8 - - - -
70B LEU* 4.7 7.2 - - - -
75B THR* 4.6 9.2 - - - -
77B VAL* 1.3 79.0 - - - +
79B LEU* 1.3 65.6 + - - +
80B ILE* 3.9 1.2 + - - +
101B VAL* 3.4 41.6 - - - +
108B THR* 5.6 0.6 + - - -
109B PRO 3.2 5.0 + - - -
110B ILE* 3.4 11.4 - - - +
111B ILE* 2.9 26.5 + - - +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B CYS* 3.7 20.4 - - - -
7B VAL 2.9 7.7 + - - +
8B VAL* 3.5 18.5 - - + -
9B VAL* 2.9 29.2 + - - +
19B LEU* 4.5 6.7 - - + -
77B VAL* 5.0 1.6 - - + -
78B SER* 1.3 74.5 - - - +
80B ILE* 1.3 60.5 + - - +
81B CYS* 3.7 5.8 + - - -
111B ILE* 3.4 31.0 - - + -
113B VAL* 4.2 9.6 - - + -
168B VAL* 3.6 27.6 - - + -
169B PHE* 3.8 23.3 - - + -
172B ALA* 4.2 13.7 - - + -
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.5 17.7 - - + +
78B SER* 4.3 1.3 - - - +
79B LEU* 1.3 71.4 - - - +
81B CYS* 1.3 56.9 + - - +
93B VAL* 4.1 15.7 - - + -
97B TRP* 3.6 28.7 - - + +
98B TYR* 3.8 30.7 - - - +
101B VAL* 4.0 10.5 - - + -
110B ILE* 3.7 27.4 - - + -
111B ILE 3.0 7.3 + - - +
112B LEU* 3.5 22.7 - - + +
113B VAL 2.8 30.8 + - - -
149B ILE* 4.1 7.6 - - + -
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Residues in contact with CYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.7 29.4 - - - -
9B VAL 2.8 14.1 + - - +
10B GLY* 3.6 18.7 - - - -
11B ASP 4.3 2.1 + - - -
14B VAL* 3.8 20.2 - - + +
16B LYS* 4.3 3.8 - - + -
19B LEU* 4.0 19.5 - - - -
79B LEU* 4.2 5.4 - - - -
80B ILE* 1.3 80.6 - - - +
82B PHE* 1.3 64.4 + - - +
89B SER* 5.0 0.7 - - - +
93B VAL* 4.9 1.2 - - - +
97B TRP* 4.9 1.9 - - - -
113B VAL* 3.2 17.5 - - - +
115B THR* 4.1 9.4 - - + -
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 4.1 5.6 - - - -
81B CYS* 1.3 76.6 - - - +
83B SER* 1.3 71.9 + - - +
84B LEU* 3.7 20.2 - - + -
89B SER* 3.6 26.5 - - - +
90B PHE* 3.5 42.6 - + + -
93B VAL* 3.9 5.2 - - + -
112B LEU* 3.8 33.9 - - + -
113B VAL 3.0 9.4 + - - -
114B GLY* 3.3 12.5 - - - -
115B THR* 2.8 27.7 + - - -
137B ILE* 4.0 9.6 - - + -
142B GLY* 4.6 0.2 - - - -
154B TYR* 3.7 25.8 - + - -
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA 5.1 0.7 - - - -
14B VAL* 3.8 20.4 - - - +
82B PHE* 1.3 78.6 - - - +
84B LEU* 1.3 59.7 + - - +
85B VAL* 3.0 23.6 + - - +
86B SER* 3.0 36.9 + - - +
89B SER* 3.0 12.6 + - - -
115B THR* 3.3 13.9 + - - -
116B LYS* 3.5 15.4 + - - +
137B ILE* 4.6 0.5 - - - +
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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