Contacts of the strand formed by residues 92 - 98 (chain B) in PDB entry 4K9N
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 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 3.9 25.1 - - + +
54B ALA 3.9 13.7 - - - +
55B ASP* 3.9 13.9 - - + -
58B ALA* 3.9 20.9 - - + -
65B ALA* 3.6 9.4 - - + -
67B ILE* 4.0 15.7 - - + -
82B LEU* 4.7 4.0 - - + -
85B ALA* 3.7 25.8 - - + -
90B SER* 2.9 18.1 + - - +
91B PRO* 1.3 81.7 - - - +
93B ILE* 1.3 62.1 + - - +
94B VAL* 3.7 2.9 - - + -
146B ALA* 4.0 0.6 - - - +
152B GLY 3.7 3.2 + - - +
153B PRO* 3.3 8.0 - - + +
154B VAL* 2.9 31.7 + - - +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ILE* 3.9 28.7 - - + -
64B PRO* 4.0 19.7 - - + -
65B ALA 2.8 15.3 + - - +
66B PHE* 3.8 24.2 - - + -
67B ILE* 2.8 30.1 + - - +
92B LEU* 1.3 73.1 - - - +
94B VAL* 1.3 59.0 + - - +
95B THR* 4.2 7.6 - - + -
139B MET* 4.4 4.7 - - - -
142B ALA* 4.2 23.1 - - + +
143B ILE* 3.9 22.9 - - + +
146B ALA* 4.0 15.5 - - + -
154B VAL* 4.0 3.6 - - + -
156B LEU* 6.1 0.2 - - + -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 5.2 1.3 - - + -
67B ILE* 3.9 24.5 - - + -
69B LEU* 3.8 28.7 - - + -
75B THR* 5.7 0.2 - - + -
82B LEU* 4.1 30.7 - - + -
92B LEU* 4.4 7.9 - - + +
93B ILE* 1.3 73.7 - - - +
95B THR* 1.3 64.2 + - - +
123B VAL* 5.9 0.4 - - + -
153B PRO* 5.0 0.9 - - + -
154B VAL* 3.0 18.4 + - - +
155B TYR* 3.2 24.5 - - + -
156B LEU* 2.8 25.5 + - - +
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PHE* 5.0 0.7 - - - -
66B PHE* 3.6 34.7 - - + -
67B ILE 2.9 19.2 + - - +
68B ASN* 3.0 19.6 + - - -
69B LEU* 2.8 28.6 + - - +
93B ILE* 4.2 6.1 - - + -
94B VAL* 1.3 79.5 - - - +
96B ALA* 1.3 61.4 + - - +
139B MET* 4.0 20.2 - - + -
156B LEU* 3.2 16.6 - - + +
158B VAL* 5.7 3.4 - - - -
163B TRP* 6.3 2.0 - - - -
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLU* 4.8 0.4 - - - -
68B ASN* 4.6 2.7 - - - +
69B LEU* 3.2 11.7 - - + +
71B SER* 4.1 10.3 - - - +
75B THR* 3.5 13.0 - - - +
95B THR* 1.3 76.8 - - - +
97B GLY* 1.3 61.8 + - - +
112B ASN* 4.9 0.9 - - - +
155B TYR* 3.4 31.6 - - + +
156B LEU 2.9 6.6 + - - +
157B SER* 3.4 3.9 - - - +
158B VAL* 3.1 26.3 + - - +
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Residues in contact with GLY 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASN* 3.3 13.3 + - - -
28B GLU* 2.8 33.8 + - - +
69B LEU 3.2 3.2 + - - -
71B SER* 3.0 31.7 + - - +
96B ALA* 1.3 73.0 - - - +
98B GLN* 1.3 59.1 + - - -
112B ASN* 5.0 1.2 + - - +
157B SER* 5.0 0.6 + - - -
158B VAL* 3.7 7.4 - - - -
163B TRP* 6.3 0.2 - - - -
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Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASN* 3.4 16.1 - - - +
71B SER* 4.9 0.4 - - - -
97B GLY* 1.3 71.9 - - - -
99B GLN* 1.3 88.3 + - - +
104B ILE* 3.7 23.4 - - + +
110B LEU 4.8 0.2 - - - -
111B THR* 3.4 7.3 - - - +
112B ASN* 2.8 51.1 + - - +
128B GLU* 2.9 27.7 + - - +
157B SER* 3.5 16.6 - - - +
158B VAL 2.9 14.4 + - - +
159B PRO* 3.6 9.0 - - + -
160B TYR* 3.1 15.6 + - - -
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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