Contacts of the strand formed by residues 86 - 95 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASN* 2.9 22.1 + - - +
84A PRO 3.3 0.2 - - - -
85A ALA* 1.3 82.2 - - - +
87A HIS* 1.3 57.6 + - - +
88A GLN* 3.2 27.8 + - - +
89A GLN* 2.9 47.5 + - - +
436A GLN* 3.3 11.6 - - - +
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Residues in contact with HIS 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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82A THR* 3.5 26.8 + - - +
83A ASN 3.0 13.4 + - - +
86A ASN* 1.3 68.4 - - - +
88A GLN* 1.3 64.9 + - + +
89A GLN 3.2 1.1 - - - -
434A LYS 2.8 28.1 + - - -
435A SER 4.0 10.1 - - - -
436A GLN* 2.9 27.9 + - - -
437A GLY* 3.5 14.8 - - - -
438A TRP* 3.4 50.7 - + + +
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Residues in contact with GLN 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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86A ASN* 3.4 22.0 + - - +
87A HIS* 1.3 84.1 + - + +
89A GLN* 1.3 60.4 + - + +
90A VAL* 3.3 15.7 + - - +
436A GLN 5.9 0.2 - - - +
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Residues in contact with GLN 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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54A PHE 4.4 0.2 + - - -
55A LYS* 3.1 56.0 + - - +
82A THR* 3.2 3.8 - - - -
83A ASN* 2.9 54.5 + - - +
86A ASN* 2.9 30.9 + - - +
88A GLN* 1.3 81.2 - - + +
90A VAL* 1.3 61.4 + - - +
91A LEU* 3.4 22.7 + - + +
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Residues in contact with VAL 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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54A PHE 5.1 0.2 - - - +
55A LYS 5.6 0.7 - - - +
57A SER 4.0 4.3 - - - +
58A SER* 2.8 34.6 + - - +
80A PRO* 4.1 12.3 - - + -
81A GLN 3.8 5.4 - - - +
82A THR* 4.0 12.8 - - + -
88A GLN 3.3 12.0 + - - +
89A GLN* 1.3 74.2 - - - +
91A LEU* 1.3 61.4 + - - +
92A ALA 3.6 22.2 - - - +
93A ASN* 3.8 18.8 - - - +
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Residues in contact with LEU 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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54A PHE* 4.0 18.6 - - + +
57A SER 4.2 1.9 - - - +
58A SER* 3.6 2.2 - - - -
59A LEU* 3.0 23.2 + - - +
81A GLN* 2.8 13.8 + - + +
82A THR 3.9 3.6 - - - -
83A ASN* 3.7 21.3 - - + +
89A GLN* 3.4 32.8 - - - +
90A VAL* 1.3 74.7 - - - +
92A ALA* 1.3 62.3 + - + +
149A LEU* 3.2 54.1 - - + +
150A GLY* 3.7 11.0 - - - +
241A LEU* 4.4 17.3 - - + +
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Residues in contact with ALA 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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58A SER* 4.6 0.4 - - - -
59A LEU* 3.1 17.9 - - + +
61A VAL* 3.9 20.9 - - + -
79A PHE 3.5 0.7 - - - +
80A PRO* 3.5 3.8 - - - +
81A GLN* 2.8 41.9 + - + +
90A VAL* 3.5 5.2 - - - +
91A LEU* 1.3 83.2 - - + +
93A ASN* 1.3 63.1 + - - +
94A VAL* 3.8 9.0 - - + -
241A LEU* 4.6 6.5 - - + -
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Residues in contact with ASN 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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58A SER* 4.0 12.5 - - - -
59A LEU 2.8 8.1 + - - -
60A GLU* 3.2 34.5 - - - +
61A VAL 2.9 24.0 + - - +
78A LEU* 4.1 23.7 - - + +
79A PHE 3.6 2.2 - - - -
80A PRO* 4.0 13.7 - - - +
90A VAL* 3.8 19.5 - - - +
92A ALA* 1.3 72.9 + - - +
94A VAL* 1.3 61.3 + - - +
95A THR* 3.7 0.9 + - - -
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Residues in contact with VAL 94 (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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61A VAL* 3.7 13.5 - - + -
78A LEU* 3.3 4.0 - - - -
79A PHE* 2.8 50.4 + - + +
81A GLN* 4.3 7.6 - - + -
92A ALA* 4.2 17.5 - - + +
93A ASN* 1.3 73.9 - - - +
95A THR* 1.3 77.5 - - - +
96A GLN* 3.0 13.4 + - - +
237A GLN* 4.8 2.0 - - - +
240A ALA* 3.5 32.5 - - + -
264A PRO* 3.8 23.6 - - + -
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Residues in contact with THR 95 (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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60A GLU* 6.1 0.2 - - - +
61A VAL 2.9 20.3 + - - -
62A PRO* 3.7 8.5 - - - +
63A LEU* 3.6 11.6 - - + +
70A ILE 3.5 19.5 - - - +
71A TYR* 3.8 9.5 - - - -
72A ASP* 3.4 17.5 + - - +
76A ARG* 3.6 27.8 - - + -
78A LEU* 3.6 15.1 - - - +
93A ASN 3.7 0.7 + - - -
94A VAL* 1.3 73.3 - - - +
96A GLN* 1.3 68.1 + - - +
264A PRO* 3.3 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