Contacts of the strand formed by residues 87 - 93 (chain A) in PDB entry 1CJY
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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20A PHE* 3.7 35.7 - - + -
22A VAL* 3.9 11.4 - - + -
48A LEU* 3.9 34.1 - - + -
49A PHE 3.6 2.5 - - - +
50A ILE* 3.9 23.1 - - + +
77A PHE* 4.5 5.6 - - + -
85A ASN 4.0 1.4 + - - -
86A VAL* 1.3 68.5 - - - +
88A GLU* 1.3 62.1 + - - +
89A ILE* 3.6 23.0 + - + +
105A ALA 3.7 1.4 - - - +
106A THR* 3.7 0.4 - - - -
107A PHE* 2.8 51.2 + - + +
109A VAL* 4.8 0.6 - - - +
134A MET* 4.2 7.0 - - + -
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Residues in contact with GLU 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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47A GLU 3.6 1.2 - - - +
48A LEU* 3.3 6.4 - - - +
49A PHE* 2.7 73.2 + - + +
51A SER* 4.4 10.6 + - - -
86A VAL* 4.2 14.7 - - + +
87A LEU* 1.3 72.7 - - - +
89A ILE* 1.3 61.3 + - - +
90A THR* 4.9 4.4 + - - +
104A THR* 5.6 9.1 - - + +
105A ALA 3.6 5.2 - - - +
106A THR* 4.6 12.1 - - - +
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Residues in contact with ILE 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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46A VAL* 3.8 17.7 - - + -
47A GLU 3.6 2.0 - - - -
48A LEU* 4.1 4.3 - - + -
87A LEU* 3.8 23.1 - - + +
88A GLU* 1.3 77.1 - - - +
90A THR* 1.3 72.2 + - - +
103A GLY 3.7 0.4 - - - +
104A THR* 3.3 1.6 - - - +
105A ALA* 2.6 49.1 + - + +
107A PHE* 4.6 2.7 - - + -
122A PHE* 3.6 33.0 - - + -
124A PHE* 5.0 0.9 - - + -
130A MET* 3.6 25.8 - - + -
132A LEU* 3.2 29.6 - - + -
134A MET* 4.7 0.4 - - + -
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Residues in contact with THR 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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46A VAL* 3.4 6.4 - - - -
47A GLU* 2.9 48.6 + - + -
88A GLU* 4.9 3.8 - - - +
89A ILE* 1.3 83.2 + - - +
91A LEU* 1.3 63.0 + - - +
92A MET* 3.3 32.9 + - + +
101A THR* 3.6 17.5 - - - +
103A GLY 3.2 5.4 - - - +
104A THR* 3.8 12.8 + - - +
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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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27A ALA* 5.3 4.5 - - + -
30A VAL* 4.5 8.5 - - + -
44A PRO* 4.6 7.4 - - + -
45A TYR 4.0 8.5 - - - +
46A VAL* 4.1 7.0 - - + -
71A TRP* 4.1 24.0 - - + -
90A THR* 1.3 72.5 - - - +
92A MET* 1.3 60.7 + - - +
101A THR* 3.7 2.9 - - - -
102A LEU* 2.8 55.1 + - + -
103A GLY 2.9 19.8 + - - +
124A PHE* 4.2 27.9 - - + -
128A THR* 4.1 25.6 - - + +
130A MET* 4.6 7.0 - - + -
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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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43A ASP 3.8 0.2 - - - +
44A PRO* 3.2 8.0 - - - +
45A TYR* 2.9 76.2 + - + +
47A GLU* 4.7 7.6 - - + +
90A THR* 3.3 33.7 - - + +
91A LEU* 1.3 75.7 - - - +
93A ASP* 1.3 58.6 + - - +
94A ALA 4.0 0.7 - - - -
99A ASP* 3.6 23.6 - - + +
100A GLU 3.3 17.7 - - - +
101A THR* 3.4 21.8 - - + +
102A LEU* 4.3 6.5 - - - +
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Residues in contact with ASP 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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32A LYS* 3.0 32.0 + - + +
40A ASP* 3.0 6.3 - - - +
42A PRO* 4.2 3.6 - - + -
43A ASP* 3.0 25.6 + - - +
45A TYR* 4.4 1.6 - - - -
92A MET* 1.3 72.6 - - - +
94A ALA* 1.3 63.0 + - - +
95A ASN* 3.2 7.7 + - - +
99A ASP* 3.5 0.3 - - - -
100A GLU* 2.8 40.6 + - + +
102A LEU* 4.2 21.3 - - + +
951A CA 2.5 22.0 - - - -
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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