Contacts of the strand formed by residues 77 - 83 (chain A) in PDB entry 2AOQ
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 GLU 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLU 3.2 25.1 - - - +
69A GLN* 3.9 11.8 - - + +
70A ASP* 3.2 11.8 - - - +
75A GLY 4.3 0.2 + - - -
76A VAL* 1.3 74.1 - - - +
78A LEU* 1.3 62.5 + - - +
79A LYS* 3.8 27.5 + - + -
116A LYS* 3.5 36.4 - - + +
119A CYS 2.9 10.8 + - - +
120A VAL* 3.3 7.4 - - + +
121A LEU 2.8 27.0 + - - -
233A CA 2.5 21.0 - - - -
5C G 3.7 9.9 + - - -
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Residues in contact with LEU 78 (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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52A GLY 5.1 0.4 - - - +
55A LEU* 4.1 7.4 - - + +
56A GLU* 4.1 39.5 - - + +
59A LEU* 3.8 16.4 - - + -
61A ALA* 4.4 8.1 - - + -
70A ASP* 2.6 20.0 + - - +
71A PHE* 4.0 11.7 - - + -
76A VAL* 4.2 0.4 - - - +
77A GLU* 1.3 71.7 - - - +
79A LYS* 1.3 70.1 + - - +
80A THR* 5.3 1.1 - - + +
121A LEU* 3.5 38.1 - - + +
123A MET* 3.8 20.6 - - + -
233A CA 2.4 28.2 - - - -
6C A 4.7 4.4 + - - +
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Residues in contact with LYS 79 (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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77A GLU* 3.8 27.5 + - + -
78A LEU* 1.3 85.1 - - - +
80A THR* 1.3 65.7 + - - +
93A THR* 3.8 19.9 - - + +
94A PHE* 3.1 28.7 + - - -
95A VAL* 4.6 13.8 + - - +
116A LYS* 5.4 4.4 - - - +
117A LEU* 4.9 11.9 - - + -
120A VAL* 4.0 9.2 - - + -
121A LEU 3.1 7.9 + - - -
122A TRP* 3.3 31.0 - - + -
123A MET* 2.9 25.4 + - - -
5C G 4.9 6.3 + - - -
6C A 4.1 18.9 + - - +
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Residues in contact with THR 80 (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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51A VAL* 4.0 10.6 - - + +
52A GLY* 3.9 18.8 + - - +
55A LEU* 3.9 26.7 - - + -
78A LEU* 5.9 1.8 - - + -
79A LYS* 1.3 81.1 - - - +
81A LEU* 1.3 61.8 + - - +
82A PRO* 4.3 4.2 - - - +
93A THR* 5.0 5.0 + - - +
122A TRP* 4.7 2.3 - - - -
123A MET* 3.3 12.6 - - + +
125A ILE* 4.2 14.3 - - + +
6C A 2.6 50.0 + - - +
7C T 5.1 0.7 + - - -
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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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80A THR* 1.3 75.9 - - - +
82A PRO* 1.3 76.3 - - + +
83A ILE* 3.4 6.9 + - + +
89A PRO* 4.3 11.2 - - + -
91A GLU 4.7 3.6 - - - +
93A THR* 3.7 23.3 - - - +
122A TRP* 4.2 27.8 - - + -
123A MET 3.1 8.6 + - - +
124A PRO* 3.4 11.4 - - + +
125A ILE* 3.0 22.2 + - - +
218A THR* 4.0 26.0 - - + +
221A ILE* 6.2 1.6 - - + -
222A LEU* 4.0 37.0 - - + -
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Residues in contact with PRO 82 (chain A).
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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80A THR* 4.3 4.3 - - - +
81A LEU* 1.3 89.9 - - + +
83A ILE* 1.3 59.0 + - - +
89A PRO* 3.3 8.3 - - - +
90A LEU* 2.8 27.7 + - + -
91A GLU* 3.9 25.4 - - + +
92A THR 5.7 1.8 - - - +
93A THR* 6.0 0.2 - - - +
125A ILE* 3.3 14.5 - - + +
127A GLY* 4.1 18.2 - - - -
6C A 5.1 0.4 - - - +
7C T 3.5 39.3 - - - +
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Residues in contact with ILE 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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81A LEU* 3.8 11.2 - - + +
82A PRO* 1.3 79.6 - - - +
84A ASN* 1.3 69.5 + - - +
87A GLY* 4.1 13.2 - - - +
88A TYR 3.1 13.9 - - - +
89A PRO* 4.2 1.6 - - + -
90A LEU* 3.5 6.6 - - - +
124A PRO* 4.2 19.1 - - + -
125A ILE* 2.9 18.8 + - - +
126A GLU* 3.8 9.1 - - + +
127A GLY 3.0 20.8 + - - -
128A SER* 4.1 0.9 + - - -
222A LEU* 3.9 29.4 - - + -
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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