Contacts of the strand formed by residues 96 - 102 (chain D) in PDB entry 1KBO
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 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D ARG 3.1 2.2 + - - -
5D ALA* 3.3 8.5 - - + -
6D LEU* 2.7 31.9 + - - +
29D LEU* 4.3 6.5 - - + -
34D TRP* 3.6 32.1 - - + -
94D ALA* 3.8 1.6 - - - +
95D ASP* 1.3 80.8 - - - +
97D VAL* 1.3 62.5 + - - +
98D ILE* 3.9 28.3 - - + -
141D LYS* 3.2 30.1 - - + +
143D VAL* 4.2 17.7 - - + -
184D LEU* 4.5 8.3 - - + -
211D LEU* 5.1 2.0 - - + -
214D ILE* 4.7 19.3 - - + -
215D TRP* 4.7 4.5 - - + -
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.3 15.0 - - + +
8D VAL* 4.3 11.2 - - + -
91D LEU* 4.2 15.0 - - + -
94D ALA* 4.3 16.6 - - + +
96D LEU* 1.3 79.0 - - - +
98D ILE* 1.3 61.2 + - - +
99D PHE* 3.3 35.0 - - + -
140D LYS* 5.1 0.9 - - + -
141D LYS 3.0 6.7 + - - -
142D ALA* 3.3 22.4 - - + +
143D VAL* 3.3 6.9 + - - +
181D PHE* 3.3 34.5 - - + -
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Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ALA* 5.3 0.7 - - + -
6D LEU 2.7 12.9 + - - +
7D ILE* 3.5 23.3 - - + -
8D VAL* 2.7 35.0 + - - +
25D ALA* 4.3 14.4 - - + -
29D LEU* 4.1 17.7 - - + -
96D LEU* 3.9 27.8 - - + -
97D VAL* 1.3 76.2 - - - +
99D PHE* 1.3 66.6 + - - +
100D GLN* 3.8 3.9 + - + +
143D VAL* 3.7 15.9 - - + +
145D SER* 4.5 6.5 - - - -
207D TRP* 3.9 23.1 - - + +
211D LEU* 4.3 11.4 - - + -
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Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D VAL* 3.4 22.7 - - + -
91D LEU* 5.7 0.2 - - + -
97D VAL* 3.3 33.4 - - + -
98D ILE* 1.3 74.4 - - - +
100D GLN* 1.3 60.0 + - - +
101D PHE* 3.3 15.3 - - + -
112D LEU* 4.0 14.6 - - + -
115D TRP* 3.4 31.2 - + - -
116D PHE* 3.6 24.2 - + - -
120D PHE* 4.9 2.5 - + - -
142D ALA* 4.4 3.6 - - + -
143D VAL 3.0 15.9 + - - -
144D LEU* 3.9 25.4 - - + -
145D SER 2.9 28.1 + - - +
176D LEU* 3.9 22.2 - - + -
181D PHE* 5.3 1.8 - + - -
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Residues in contact with GLN 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 4.6 12.6 - - + -
8D VAL 2.7 13.4 + - - +
9D LEU* 3.3 16.7 - - + +
10D ALA* 2.9 22.3 + - - +
18D ASN* 2.9 41.3 + - - +
21D MET* 3.8 28.6 - - + +
22D LYS* 4.5 4.7 - - + +
98D ILE* 3.8 3.9 + - + +
99D PHE* 1.3 70.9 - - - +
101D PHE* 1.3 66.8 + - - +
112D LEU* 5.4 0.2 - - - +
145D SER* 2.5 46.1 + - - -
147D THR* 4.1 10.5 - - - +
207D TRP* 4.2 2.9 + - - -
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Residues in contact with PHE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA* 4.0 18.6 - - + +
18D ASN* 3.0 13.9 + - - +
99D PHE* 3.3 30.3 - - + -
100D GLN* 1.3 75.9 - - - +
102D PRO* 1.3 84.3 - - + +
103D LEU* 4.6 2.0 - - + -
107D GLY 4.2 5.8 - - - -
108D VAL* 3.7 30.5 - - + -
109D PRO* 3.3 13.5 - - + -
112D LEU* 3.9 13.0 - - + -
144D LEU* 4.2 13.0 - - + -
145D SER 3.1 15.0 + - - +
146D ILE* 3.3 52.2 - - + -
147D THR 3.3 1.9 + - - -
171D ILE* 5.0 2.0 - - + -
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Residues in contact with PRO 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA 3.5 15.9 - - - +
11D HIS* 4.0 11.4 - - + -
18D ASN* 3.4 17.7 - - - +
101D PHE* 1.3 102.2 - - + +
103D LEU* 1.3 65.0 + - - +
104D GLN* 3.2 29.0 + - - +
109D PRO* 3.7 2.8 - - + +
147D THR* 3.3 13.0 - - - +
604D FAD 3.4 33.0 - - - +
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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