Contacts of the strand formed by residues 87 - 94 (chain A) in PDB entry 5IXC
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.6 4.4 - - - +
52A SER* 2.9 46.5 + - - +
85A LYS* 4.6 17.7 - - + -
86A ASN* 1.3 75.5 - - - +
88A LEU* 1.3 64.8 + - - +
89A GLU* 3.7 2.2 + - + +
108A LEU* 4.1 33.7 - - + -
109A TYR 3.6 9.9 - - - +
110A ASP* 4.8 10.1 - - + +
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Residues in contact with LEU 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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24A LEU* 5.1 1.6 - - + -
26A VAL* 4.2 14.6 - - + -
49A LEU* 4.5 4.5 - - + -
50A GLN 3.4 26.0 - - - +
51A LEU* 4.0 11.1 - - + +
78A PHE* 4.1 22.7 - - + -
86A ASN 4.1 0.6 + - - -
87A VAL* 1.3 73.1 - - - +
89A GLU* 1.3 61.8 + - - +
90A LEU* 3.7 24.7 + - + +
107A VAL 3.7 1.2 - - - +
108A LEU* 3.5 2.1 - - - -
109A TYR* 2.8 48.7 + - + +
111A ILE* 4.0 14.1 - - + +
138A PHE* 3.7 31.6 - - + -
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Residues in contact with GLU 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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48A ILE* 3.6 2.0 - - - +
49A LEU* 3.5 2.3 - - - -
50A GLN* 2.7 72.7 + - + +
52A SER 6.2 0.2 - - - +
87A VAL* 3.7 2.9 + - + +
88A LEU* 1.3 72.1 - - - +
90A LEU* 1.3 63.5 + - - +
91A SER* 3.7 19.1 + - - -
93A TYR* 5.0 4.2 + - - -
106A LYS* 3.3 30.0 + - + +
107A VAL 3.5 4.0 - - - +
108A LEU* 3.5 25.6 - - + -
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Residues in contact with LEU 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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26A VAL* 5.5 0.4 - - + -
28A VAL* 6.0 0.2 - - + -
47A VAL* 4.5 3.8 - - + -
48A ILE 3.3 3.1 - - - +
49A LEU* 3.4 26.2 - - + -
88A LEU* 3.7 30.7 - - + +
89A GLU* 1.3 74.7 - - - +
91A SER* 1.3 61.3 - - - +
105A PHE* 4.6 1.6 - - - -
106A LYS* 3.8 0.5 - - - -
107A VAL* 2.9 66.2 + - + +
109A TYR* 5.6 2.7 - - + -
124A PHE* 4.6 9.2 - - + -
134A LEU* 3.3 28.7 - - + -
136A VAL* 4.3 18.6 - - + -
138A PHE* 4.6 8.3 - - + -
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Residues in contact with SER 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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46A TYR 3.9 0.2 - - - +
47A VAL* 3.3 5.8 - - - +
48A ILE* 2.8 40.7 + - - +
89A GLU* 3.7 20.3 + - - -
90A LEU* 1.3 77.3 - - - +
92A ILE* 1.3 65.9 + - - +
93A TYR* 3.3 20.0 + - - -
103A ILE* 3.5 15.3 - - - -
105A PHE* 3.2 13.5 - - - -
106A LYS* 4.2 5.8 - - - -
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Residues in contact with ILE 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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31A ALA* 4.0 15.9 - - + -
34A LEU* 3.9 32.5 - - + -
45A PRO* 4.0 9.9 - - + -
46A TYR 3.4 10.3 - - - +
47A VAL* 4.2 13.2 - - + -
72A TRP* 4.6 2.5 - - + -
91A SER* 1.3 77.4 - - - +
93A TYR* 1.3 61.5 - - - +
103A ILE* 3.7 2.1 - - - -
104A CYS* 2.8 43.9 + - - -
105A PHE* 2.9 48.1 + - + +
133A GLU 5.1 0.4 - - - +
134A LEU* 4.0 14.1 - - + -
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Residues in contact with TYR 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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45A PRO* 3.1 6.9 - - - +
46A TYR* 2.9 57.5 + + + +
48A ILE* 3.8 28.8 - - + +
89A GLU* 5.0 3.8 + - - -
91A SER* 3.3 27.7 + - - -
92A ILE* 1.3 77.3 - - - +
94A ASP* 1.3 59.7 + - - +
95A GLU 3.9 1.1 + - - -
101A ASP* 3.7 23.8 - - + -
102A ASP 3.4 3.8 - - - -
103A ILE* 3.5 40.5 - - + +
104A CYS* 4.3 3.6 - - - -
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Residues in contact with ASP 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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35A ARG 5.3 0.2 - - - +
36A TRP 5.0 0.5 - - - -
37A ALA* 3.5 29.0 + - - +
42A GLU 4.7 1.3 - - - +
43A ALA* 3.6 17.9 - - + +
44A ASP* 3.0 30.5 + - - +
45A PRO* 4.5 1.1 - - - -
93A TYR* 1.3 71.1 - - - +
95A GLU* 1.3 70.2 + - - +
96A ASP* 3.6 3.2 + - - +
101A ASP* 3.6 17.8 - - - +
102A ASP* 2.9 26.9 + - + +
104A CYS* 4.3 7.6 - - + -
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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