Contacts of the strand formed by residues 86 - 95 (chain B) in PDB entry 4OE4
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 ASN 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASN* 2.8 16.7 + - - +
84B PRO 3.2 0.8 + - - -
85B ALA* 1.3 83.5 - - - +
87B HIS* 1.3 57.9 + - - +
88B GLN* 3.2 13.0 + - - +
89B GLN* 3.0 50.3 + - - +
436B GLN* 3.2 22.1 + - - +
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Residues in contact with HIS 87 (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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82B THR* 3.3 32.3 - - - +
83B ASN 3.0 12.4 + - - +
86B ASN* 1.3 67.4 - - - +
88B GLN* 1.3 68.6 + - + +
89B GLN 3.1 2.5 - - - -
434B LYS 2.7 28.5 + - - -
435B SER 3.8 11.4 - - - -
436B GLN* 3.0 21.8 + - - -
437B GLY* 3.5 12.3 - - - -
438B TRP* 3.4 45.4 - + + +
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Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASN* 3.1 9.1 + - - +
87B HIS* 1.3 85.6 + - + +
89B GLN* 1.3 59.6 + - - +
90B VAL* 3.5 10.7 + - - +
436B GLN 4.7 0.4 + - - -
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE 5.8 0.2 - - - +
55B LYS* 3.2 49.5 - - - +
82B THR* 3.2 4.9 - - - -
83B ASN* 3.0 57.0 + - + +
86B ASN* 3.0 29.4 + - - +
88B GLN* 1.3 78.5 - - - +
90B VAL* 1.3 65.2 + - - +
91B LEU* 3.7 13.3 - - + +
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE 4.9 0.5 - - - +
55B LYS 5.6 0.7 - - - +
57B SER 3.9 4.0 - - - +
58B SER* 2.9 37.7 + - - +
80B PRO* 4.5 11.0 - - + -
81B GLN 3.8 5.8 - - - +
82B THR* 4.1 13.5 - - + -
87B HIS 5.5 0.2 - - - +
88B GLN 3.5 9.3 + - - +
89B GLN* 1.3 76.1 - - - +
91B LEU* 1.3 58.7 + - - +
92B ALA 3.5 29.8 - - - +
93B ASN* 3.9 15.7 - - - +
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Residues in contact with LEU 91 (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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54B PHE* 4.1 20.9 - - + +
57B SER 4.2 1.6 - - - +
58B SER* 3.6 1.8 - - - -
59B LEU* 3.0 22.6 + - - +
81B GLN* 3.0 13.0 + - + +
82B THR 4.0 2.9 - - - -
83B ASN* 3.8 21.3 - - + +
89B GLN* 3.7 26.2 - - + +
90B VAL* 1.3 73.9 - - - +
92B ALA* 1.3 62.5 + - + +
149B LEU* 3.3 58.1 - - + +
150B GLY* 3.5 12.3 - - - +
241B LEU* 4.2 18.1 - - + +
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Residues in contact with ALA 92 (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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59B LEU 3.1 14.4 - - - +
61B VAL* 3.8 21.3 - - + -
79B PHE 3.6 0.3 - - - +
80B PRO* 3.5 0.5 - - - +
81B GLN* 2.8 49.3 + - + +
90B VAL* 3.4 12.4 - - - +
91B LEU* 1.3 83.1 - - + +
93B ASN* 1.3 59.5 + - - +
94B VAL* 3.8 4.9 - - + -
241B LEU* 4.3 8.5 - - + -
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Residues in contact with ASN 93 (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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58B SER* 4.0 17.7 - - - +
59B LEU 2.9 10.1 + - - +
60B GLU* 3.4 9.0 - - + +
61B VAL 3.0 23.0 + - - +
78B LEU* 3.9 31.7 - - + +
79B PHE 3.5 3.0 + - - -
80B PRO* 4.0 15.2 - - - +
90B VAL* 3.9 16.9 - - - +
92B ALA* 1.3 70.7 + - - +
94B VAL* 1.3 63.3 + - - +
95B THR 3.6 1.4 + - - -
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Residues in contact with VAL 94 (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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61B VAL* 3.7 13.0 - - + -
78B LEU* 3.2 5.6 - - - -
79B PHE* 2.6 51.0 + - + +
81B GLN* 4.2 17.7 - - + -
92B ALA* 4.2 9.6 - - + -
93B ASN* 1.3 73.4 - - - +
95B THR* 1.3 69.3 + - - +
96B GLN* 3.4 9.5 + - - +
237B GLN* 4.7 2.0 - - - +
240B ALA* 3.6 30.5 - - + -
264B PRO* 3.7 33.7 - - + -
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Residues in contact with THR 95 (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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60B GLU* 5.8 0.5 - - - +
61B VAL 2.7 23.0 + - - -
62B PRO* 3.7 7.9 - - - +
63B LEU* 3.6 9.1 - - + +
70B ILE 3.7 10.3 - - - +
71B TYR* 3.6 8.7 - - - +
72B ASP* 3.2 29.3 + - - +
76B ARG* 3.5 29.2 - - + -
78B LEU* 3.8 12.5 - - - +
93B ASN 3.6 1.3 + - - -
94B VAL* 1.3 72.2 - - - +
96B GLN* 1.3 67.8 + - - +
264B PRO* 3.5 21.8 - - - +
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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