Contacts of the strand formed by residues 80 - 87 (chain A) in PDB entry 2P80
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 TYR 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.9 8.4 - - + +
12A LEU* 4.1 24.1 - - + +
36A PRO* 4.8 4.0 - - + -
37A LYS 3.5 5.4 + - - -
38A VAL* 3.3 25.2 - - + -
39A VAL* 2.8 31.2 + - - +
75A VAL* 5.7 0.4 - - - -
78A ASP 2.9 16.8 - - - -
79A ASP* 1.3 76.2 - - - +
81A LEU* 1.3 59.8 + - - +
82A GLU 3.7 0.3 + - - -
123A ARG* 3.8 24.7 - - - -
124A PHE 3.3 6.7 - - - +
125A LYS* 2.9 62.7 + - + +
329B ASP* 3.2 29.5 + - - -
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Residues in contact with LEU 81 (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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39A VAL* 3.7 4.5 - - - -
41A PHE* 4.3 12.6 - - + -
73A MET* 4.0 36.3 - - + -
75A VAL* 4.3 19.7 - - + -
79A ASP 4.0 1.6 + - - -
80A TYR* 1.3 71.6 - - - +
82A GLU* 1.3 65.2 + - - +
83A LEU* 3.6 28.0 - - + +
99A PHE* 5.5 4.0 - - + -
122A LEU 3.5 1.8 - - - +
123A ARG* 3.2 2.7 - - - -
124A PHE* 3.0 67.0 + - + -
154A ILE* 4.3 14.6 - - + -
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Residues in contact with GLU 82 (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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14A ARG* 4.9 5.0 + - - +
38A VAL* 3.9 19.0 - - + +
39A VAL 2.8 15.7 + - - +
40A GLU* 3.3 26.1 - - + +
41A PHE 3.0 23.4 + - - +
81A LEU* 1.3 74.7 - - - +
83A LEU* 1.3 59.9 + - - +
84A THR 4.0 0.5 + - - -
121A ILE* 3.6 24.7 - - + +
122A LEU 3.5 3.1 - - - +
123A ARG* 3.3 31.9 + - + +
334B VAL* 3.4 19.5 - - - +
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Residues in contact with LEU 83 (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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41A PHE* 3.0 32.8 - - + +
43A MET* 3.8 38.1 - - + +
73A MET* 4.6 2.2 - - - -
81A LEU* 3.6 17.9 - - + +
82A GLU* 1.3 75.3 - - - +
84A THR* 1.3 65.3 + - - +
85A LEU* 3.5 17.1 + - + +
97A ILE* 3.9 33.9 - - + -
99A PHE* 4.0 13.2 - - + -
120A THR* 3.9 0.5 - - - +
121A ILE* 3.6 2.0 - - - -
122A LEU* 3.1 33.4 + - + +
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Residues in contact with THR 84 (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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41A PHE 3.0 8.1 + - - -
42A THR* 3.2 23.8 + - + +
43A MET 3.1 21.7 + - - -
82A GLU 4.0 1.1 + - - -
83A LEU* 1.3 71.6 - - - +
85A LEU* 1.3 57.9 + - - +
86A ILE* 4.1 21.8 - - + -
119A LYS* 4.3 13.0 - - + +
120A THR 3.2 13.9 - - - +
121A ILE* 2.9 32.7 - - + +
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Residues in contact with LEU 85 (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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43A MET* 3.0 31.6 - - + +
45A ILE* 3.2 25.6 - - + -
64A PHE* 3.4 35.7 - - + -
83A LEU* 3.5 20.3 + - + +
84A THR* 1.3 71.5 - - - +
86A ILE* 1.3 66.2 + - - +
96A ASN* 4.9 7.9 - - - -
97A ILE* 4.8 13.7 - - + -
112A THR* 5.0 3.6 - - + +
114A ILE* 3.5 18.8 - - + -
119A LYS* 2.9 25.7 - - - +
120A THR* 3.1 17.4 + - + +
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Residues in contact with ILE 86 (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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42A THR* 3.8 26.9 - - + -
43A MET 3.2 4.4 + - - -
44A VAL* 3.4 24.5 - - + -
45A ILE* 3.0 26.7 + - - +
84A THR* 4.1 5.6 - - + -
85A LEU* 1.3 86.6 - - - +
87A ASN* 1.3 68.1 + - - +
88A PRO* 3.2 8.7 - - + +
114A ILE* 4.2 2.2 - - - -
118A GLU 4.9 0.9 - - - +
119A LYS* 3.3 35.7 - - + +
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Residues in contact with ASN 87 (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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45A ILE* 4.3 4.1 - - + +
86A ILE* 1.3 76.2 - - - +
88A PRO* 1.3 54.6 - - - +
91A ASN* 2.5 38.6 + - - +
93A LEU 3.1 25.9 + - - -
95A HIS* 3.5 12.9 - - - -
114A ILE* 3.3 35.9 + - + +
115A ASN 4.3 1.6 - - - +
116A PRO* 3.5 14.5 - - - +
117A GLY* 2.8 32.1 + - - -
118A GLU 3.2 15.1 + - - +
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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