Contacts of the strand formed by residues 78 - 83 (chain A) in PDB entry 3ORY
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 LYS 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLY* 4.3 21.3 + - - +
26A LYS 2.8 16.1 + - - +
27A ILE* 3.2 19.5 - - + +
28A ILE 3.0 21.0 + - - -
76A GLY 4.3 5.6 - - - +
77A ILE* 1.3 74.6 - - - +
79A PRO* 1.3 66.6 - - - +
300A TRP* 3.5 30.5 - - + +
337A ASN 3.6 21.1 - - - +
338A ILE* 4.3 27.6 + - + +
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Residues in contact with PRO 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.5 6.5 - - - +
30A ILE* 3.8 23.1 - - + -
69A THR* 4.2 9.4 - - + -
72A ILE* 4.0 16.2 - - + -
73A VAL* 3.8 23.8 - - + -
77A ILE* 3.2 14.6 - - + +
78A LYS* 1.3 82.9 - - - +
80A VAL* 1.3 60.8 + - - +
81A TYR* 4.7 5.8 - - + -
148A ILE* 3.7 14.0 - - + +
149A PRO* 3.7 6.6 - - - +
300A TRP* 2.9 27.0 + - - +
338A ILE* 4.7 1.3 - - + -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 4.0 19.5 - - + -
28A ILE 3.0 11.5 + - - +
29A VAL* 3.2 23.1 - - + -
30A ILE* 2.7 32.4 + - - +
79A PRO* 1.3 75.2 - - - +
81A TYR* 1.3 70.1 + - - +
149A PRO* 3.5 22.7 - - + +
151A VAL* 4.1 18.2 - - + -
170A ALA* 5.3 0.2 - - + -
298A ILE* 3.8 32.5 - - + -
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Residues in contact with TYR 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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29A VAL* 4.8 0.4 - - - -
30A ILE* 3.2 52.8 - - + +
32A GLY* 4.3 11.7 - - - -
35A ALA* 4.1 9.9 - - + -
39A PHE* 4.7 7.8 - - - -
65A LEU* 3.5 21.8 - - + +
69A THR* 2.8 33.3 + - + +
72A ILE* 4.6 4.0 - - - +
79A PRO* 4.7 2.0 - - + -
80A VAL* 1.3 82.5 - - - +
82A VAL* 1.3 61.3 + - - +
83A PHE* 4.0 20.6 - + + -
143A LEU* 3.8 25.8 - - + -
148A ILE* 4.1 13.5 - - + -
149A PRO 3.1 7.3 + - - -
150A TRP* 3.0 8.9 - - + -
151A VAL* 2.8 22.6 + - - +
193A THR* 5.6 0.9 - - - +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.8 13.7 - - + -
30A ILE 2.9 16.7 + - - +
31A ASP* 3.8 10.5 - - - +
32A GLY* 2.8 27.5 + - - -
33A TYR 4.6 0.2 + - - -
81A TYR* 1.3 75.6 - - - +
83A PHE* 1.3 64.3 + - - +
84A ASP 4.3 0.3 + - - -
151A VAL* 3.4 16.4 - - + +
153A ALA* 3.9 7.6 - - + -
157A GLY* 3.6 20.1 - - - +
160A GLN* 3.7 37.5 - - + -
161A ALA* 3.8 18.6 - - + -
164A ILE* 4.9 0.2 - - + -
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Residues in contact with PHE 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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32A GLY* 3.7 25.4 - - - -
33A TYR* 3.9 19.5 - + + -
36A LEU* 4.0 21.8 - - + -
65A LEU* 5.6 1.3 - - + -
81A TYR* 4.0 8.1 - + + -
82A VAL* 1.3 73.6 - - - +
84A ASP* 1.3 64.0 + - - +
136A VAL* 4.1 9.9 - - + -
139A ALA* 4.4 9.9 - - + -
140A LYS* 3.6 40.4 - - + +
143A LEU* 3.8 22.9 - - + -
150A TRP* 3.7 33.2 - + + -
151A VAL 2.9 9.8 + - - +
152A GLN* 3.3 3.6 + - - +
153A ALA* 2.8 30.9 + - - +
157A GLY* 4.6 0.7 - - - -
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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