Contacts of the strand formed by residues 87 - 93 (chain A) in PDB entry 3ORO
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 LEU 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL* 4.3 26.0 - - + -
42A LEU* 5.8 2.5 - - + +
79A GLU* 3.2 1.9 - - - -
80A ALA* 2.7 43.3 + - + +
82A THR* 3.6 28.5 - - + +
85A GLY 4.2 1.1 - - - +
86A PRO* 1.3 71.2 - - - +
88A PRO* 1.3 80.8 - - + +
89A TYR* 3.4 6.8 - - + -
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Residues in contact with PRO 88 (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 VAL* 3.7 15.2 - - - +
42A LEU* 4.7 9.8 + - + -
53A TYR* 4.2 27.1 - - + +
56A PHE* 3.7 31.2 - - + -
57A ARG* 4.8 23.6 - - + +
60A ALA* 5.2 2.9 - - + -
78A GLY 3.3 9.6 - - - +
79A GLU* 4.2 6.3 - - + -
86A PRO 3.5 9.9 - - - +
87A LEU* 1.3 89.6 - - + +
89A TYR* 1.3 59.8 + - - +
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Residues in contact with TYR 89 (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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11A TYR* 6.3 1.3 - + - -
39A VAL* 4.8 7.4 - - + -
40A LYS 3.4 10.1 - - - +
41A VAL* 4.1 10.5 - - + -
56A PHE* 4.1 3.0 - - - -
60A ALA* 4.2 2.9 - - - +
76A ASP* 2.8 29.4 + - - -
77A THR* 3.4 11.9 + - - -
78A GLY* 2.9 53.3 + - - +
79A GLU 3.6 2.0 - - - -
80A ALA* 3.4 26.2 - - + -
87A LEU* 3.4 15.0 - - + +
88A PRO* 1.3 75.1 - - - +
90A ILE* 1.3 68.9 + - - +
91A VAL* 3.8 23.8 - - + -
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Residues in contact with ILE 90 (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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38A ALA 3.6 1.2 - - - +
39A VAL* 3.4 4.3 - - - +
40A LYS* 2.7 69.3 + - + +
56A PHE* 4.6 4.9 - - + -
59A GLU* 4.4 6.7 - - + +
60A ALA* 3.8 33.2 - - + +
63A ALA* 4.5 6.3 - - + -
74A VAL* 4.0 30.7 - - + -
76A ASP 3.6 3.8 - - - +
77A THR* 4.1 4.3 - - + -
89A TYR* 1.3 80.9 - - - +
91A VAL* 1.3 69.0 + - - +
92A MET* 4.6 12.7 - - + +
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Residues in contact with VAL 91 (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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11A TYR* 4.0 28.3 - - + +
35A ARG* 5.8 0.4 - - - +
37A VAL* 3.8 33.9 - - + -
38A ALA 3.5 3.1 - - - +
39A VAL* 4.4 15.9 - - + -
74A VAL* 3.7 2.6 - - - +
75A TYR* 2.8 38.3 + - + -
76A ASP* 2.7 25.0 + - + +
89A TYR* 3.8 23.1 - - + -
90A ILE* 1.3 75.9 - - - +
92A MET* 1.3 59.9 + - - +
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Residues in contact with MET 92 (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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25A VAL* 4.1 10.3 - - + -
37A VAL* 3.5 6.4 - - - +
38A ALA* 2.8 43.2 + - + +
40A LYS* 3.8 38.4 - - + -
72A VAL* 3.9 11.9 - - + -
73A ALA 3.1 16.8 - - - +
74A VAL* 4.1 10.8 - - + -
75A TYR* 3.6 9.0 - - - -
90A ILE* 4.6 8.5 - - + +
91A VAL* 1.3 74.9 - - - +
93A GLU* 1.3 59.5 + - - +
94A TYR 3.4 0.5 + - - -
155A MET* 5.8 3.6 - - - -
156A ASP 6.3 0.7 - - - -
340A AGS 3.3 48.7 - - + +
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Residues in contact with GLU 93 (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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38A ALA* 4.1 0.2 - - - +
68A HIS 5.3 0.3 - - - +
71A ILE 3.5 8.0 - - - +
72A VAL* 3.7 10.8 - - + +
73A ALA* 2.8 42.2 + - - +
75A TYR* 3.4 28.8 - - + +
92A MET* 1.3 71.4 - - - +
94A TYR* 1.3 72.3 + - - +
95A VAL* 3.7 2.9 + - + +
153A LYS* 2.8 35.8 + - - +
340A AGS 2.9 24.4 + - - -
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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