Contacts of the strand formed by residues 83 - 91 (chain A) in PDB entry 5EYI
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 VAL 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 5.3 2.0 - - - +
63A ALA* 4.0 17.5 - - + -
64A CYS 3.9 9.6 - - - +
65A ILE* 4.1 13.0 - - + +
81A GLY 4.2 1.1 + - - +
82A VAL* 1.3 79.3 - - - +
84A SER* 1.3 62.4 + - - +
85A TYR* 3.5 23.6 - - - +
86A TYR* 3.7 34.8 - - + +
303A PG0 3.6 13.5 - - - +
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 2.7 31.5 + - - -
54A LEU* 4.4 1.7 - - - +
64A CYS 2.9 12.7 + - - -
66A GLY* 3.8 4.0 + - - -
67A ALA 2.6 40.6 + - - -
69A TYR* 3.8 12.7 - - - -
78A GLY* 4.3 3.1 - - - -
79A THR 4.9 0.7 + - - -
82A VAL 3.4 1.8 + - - -
83A VAL* 1.3 74.2 - - - +
85A TYR* 1.3 69.2 + - - +
303A PG0 3.4 18.2 - - - +
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Residues in contact with TYR 85 (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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3A SER* 3.7 19.7 - - - +
4A SER* 4.0 7.9 - - - -
5A PRO* 3.4 33.2 - - + +
9A VAL* 3.9 18.7 - - - +
52A ALA* 4.9 0.4 - - + -
53A SER 3.6 10.5 - - - +
54A LEU* 5.0 3.1 - - - +
64A CYS* 2.9 55.8 + - + +
67A ALA* 4.0 11.2 - - + +
68A GLY 3.6 21.1 + - - -
69A TYR* 3.8 10.5 - - + -
83A VAL* 3.5 10.2 - - - +
84A SER* 1.3 90.2 - - - +
86A TYR* 1.3 69.1 + - - +
87A LEU* 3.6 19.5 - - + -
103A PHE* 4.3 1.4 - - - -
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Residues in contact with TYR 86 (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 3.5 0.6 - - - +
52A ALA* 3.3 6.8 - - - -
53A SER* 2.7 47.6 + - - +
54A LEU 3.6 19.5 - - - -
55A ARG 3.6 13.7 - - - +
56A PRO* 3.6 33.2 - - + +
61A SER* 4.1 23.1 - - - -
62A ARG 3.2 7.0 - - - +
63A ALA* 3.5 30.3 - - + +
83A VAL* 3.7 26.3 - - + +
85A TYR* 1.3 75.9 - - - +
87A LEU* 1.3 63.0 + - - +
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Residues in contact with LEU 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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5A PRO* 4.3 9.0 - - + -
9A VAL* 3.9 18.2 - - + -
13A LEU* 4.2 12.1 - - + -
38A VAL* 5.7 0.2 - - + -
50A LEU* 4.1 18.6 - - + -
51A VAL 3.3 9.0 - - - +
52A ALA* 4.0 13.2 - - + -
60A TYR 3.9 0.2 - - - +
61A SER* 3.4 0.9 - - - -
62A ARG 2.9 31.6 + - - +
64A CYS* 3.9 9.6 - - - -
85A TYR* 3.6 20.0 - - + -
86A TYR* 1.3 79.3 - - - +
88A THR* 1.3 63.4 + - - +
98A LEU* 3.6 19.0 - - + +
205A PHE* 3.7 30.1 - - + -
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Residues in contact with THR 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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49A ARG 3.6 1.9 - - - +
50A LEU* 3.4 3.6 - - - -
51A VAL* 2.7 38.1 + - - +
53A SER* 4.9 2.1 + - - -
57A ILE* 3.3 22.0 - - + +
58A HIS* 3.9 20.9 - - + -
60A TYR* 4.6 3.6 - - + -
61A SER* 2.7 29.9 + - - +
87A LEU* 1.3 75.8 - - - +
89A LYS* 1.3 62.0 + - - +
90A PHE* 3.7 26.4 + - + -
95A ALA* 4.5 9.6 - - + -
96A GLN 5.7 0.2 - - - +
98A LEU* 4.7 0.4 - - - -
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Residues in contact with LYS 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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13A LEU* 3.6 31.6 + - + +
15A PHE* 4.1 24.7 - - + -
49A ARG 3.5 3.8 - - - -
50A LEU* 4.0 11.2 - - + +
87A LEU 4.3 0.4 - - - -
88A THR* 1.3 73.2 - - - +
90A PHE* 1.3 59.9 + - - +
91A VAL* 3.8 26.9 - - + -
95A ALA* 3.4 2.6 - - - +
96A GLN* 2.8 44.7 + - + +
98A LEU* 4.0 30.3 - - + +
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Residues in contact with PHE 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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15A PHE* 4.7 1.9 - - - -
42A ASN* 3.6 18.2 - - - -
47A PRO 3.5 12.3 - - - +
48A ASP* 3.2 4.2 - - - +
49A ARG* 2.8 83.7 + - + +
51A VAL* 4.1 5.4 - - + -
57A ILE* 4.4 2.7 - - + -
58A HIS* 4.8 11.2 - + + -
88A THR* 3.7 32.8 - - + -
89A LYS* 1.3 75.3 - - - +
91A VAL* 1.3 63.8 + - - +
93A GLY 3.6 14.8 - - - -
94A GLU 3.3 5.4 - - - +
95A ALA* 3.5 30.1 - - + -
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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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15A PHE* 5.7 1.6 - - + -
48A ASP* 3.3 11.4 - - + +
89A LYS* 3.8 24.0 - - - -
90A PHE* 1.3 76.4 - - - +
92A LYS* 1.3 74.4 + - + +
93A GLY 3.2 0.7 - - - -
94A GLU* 2.9 21.9 + - - +
96A GLN* 3.4 36.3 - - + +
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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