Contacts of the strand formed by residues 95 - 102 (chain A) in PDB entry 5KJH
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 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.7 9.2 - - - -
60A THR* 4.1 2.2 - - + -
61A SER 3.8 12.4 + - - +
62A LYS* 2.7 36.2 + - - +
63A LYS* 4.7 2.4 - - - +
64A HIS 6.3 0.2 - - - -
89A ASP* 2.8 34.1 + - - +
93A GLU* 3.5 6.6 + - - +
94A ALA* 1.3 72.8 - - - +
96A CYS* 1.3 65.6 + - - +
113A ILE* 3.4 24.0 - - + +
114A ALA 3.4 7.5 - - - +
115A GLY 3.4 12.1 + - - -
121A LYS* 2.7 22.3 + - - +
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Residues in contact with CYS 96 (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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41A PHE* 3.6 41.1 - - + +
42A ASP* 3.9 6.6 - - - +
60A THR* 4.6 3.8 - - - +
94A ALA 5.2 1.1 - - - +
95A ASN* 1.3 76.9 - - - +
97A ALA* 1.3 62.1 + - - +
114A ALA 3.0 5.7 + - - -
115A GLY* 4.4 4.7 - - - -
141A ILE 3.3 26.5 - - - -
142A ASN* 3.9 23.2 - - - +
328A PHE* 4.2 10.8 - - + -
330A ARG* 3.9 14.0 + - - -
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Residues in contact with ALA 97 (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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42A ASP* 3.9 4.7 - - - -
60A THR* 4.6 2.4 - - - +
96A CYS* 1.3 81.6 - - - +
98A SER* 1.3 60.7 + - - +
113A ILE* 3.3 8.7 - - - +
114A ALA* 2.9 36.3 + - + +
141A ILE* 4.6 0.9 - - + -
142A ASN 3.9 5.8 - - - +
143A ASP* 3.8 37.7 - - - +
144A LEU* 3.9 10.1 - - + +
330A ARG* 5.7 0.4 - - - +
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Residues in contact with SER 98 (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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42A ASP* 2.7 24.0 + - - +
44A LYS* 2.9 41.1 + - - +
58A ALA 4.9 2.6 + - - -
60A THR* 3.5 11.0 + - - -
97A ALA* 1.3 76.2 - - - +
99A CYS* 1.3 62.1 + - - +
111A LEU* 4.3 7.9 - - - +
112A CYS 3.0 15.7 - - - -
113A ILE* 3.5 16.4 - - - -
143A ASP* 5.9 0.2 + - - -
144A LEU* 3.8 12.4 - - - +
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Residues in contact with CYS 99 (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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44A LYS* 4.6 10.5 - - + +
98A SER* 1.3 76.5 - - - +
100A TRP* 1.3 62.1 + - - +
111A LEU* 3.8 5.2 - - - +
112A CYS* 2.9 44.2 + - - +
144A LEU* 3.8 24.5 - - + +
145A ALA* 4.3 0.2 - - - -
146A THR* 3.2 32.8 - - - +
154A ILE* 3.9 21.1 - - - -
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Residues in contact with TRP 100 (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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44A LYS* 2.8 36.2 + - + +
45A PHE 3.4 21.6 - - - -
46A TYR* 3.4 34.8 - + + -
47A PRO* 3.8 19.2 - - + +
48A TYR* 3.8 5.0 + - + -
56A VAL* 4.7 1.3 - - + -
57A PHE 4.3 4.3 - - - -
58A ALA* 3.5 31.0 - - + -
67A ILE* 4.6 9.2 - - + -
99A CYS* 1.3 75.5 - - - +
101A SER* 1.3 60.6 + - - +
109A PRO* 3.9 5.6 - - + -
110A LEU 3.4 21.8 - - - -
111A LEU* 3.9 18.1 - - + +
125A VAL* 3.9 25.6 - - + -
146A THR* 2.7 32.8 + - - +
244B PHE* 3.9 16.4 - + - -
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Residues in contact with SER 101 (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* 4.0 6.1 - - - -
48A TYR* 4.3 4.0 - - - -
100A TRP* 1.3 74.6 - - - +
102A LYS* 1.3 76.3 + - - +
109A PRO* 3.8 2.4 - - - +
110A LEU* 2.8 32.1 + - - +
112A CYS* 4.4 3.1 - - - -
151A PRO 2.7 27.9 + - - -
152A TYR* 3.9 1.6 - - - -
154A ILE* 3.9 11.7 - - - +
168A LEU* 3.4 30.5 - - - +
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Residues in contact with LYS 102 (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* 3.4 21.1 - - - +
48A TYR* 3.5 23.1 - - + -
101A SER* 1.3 86.1 + - - +
103A ASP* 1.3 64.4 + - - +
104A PRO* 3.4 3.6 - - - +
107A ASP* 2.8 38.4 + - - +
108A GLN 3.4 8.3 - - - +
110A LEU* 3.6 9.3 - - - +
151A PRO* 4.1 21.6 + - + +
152A TYR* 3.3 27.4 + - + -
168A LEU* 4.9 0.7 - - - +
237B HIS* 2.8 32.3 + - - +
238B LEU 4.7 0.6 - - - -
239B SER* 3.9 7.8 + - - +
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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