Contacts of the strand formed by residues 204 - 213 (chain A) in PDB entry 1KIT
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 ALA 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A TRP 3.3 2.8 - - - +
67A LEU* 3.6 7.2 - - - -
68A VAL* 2.9 34.5 + - - +
100A MET* 4.6 3.1 - - - -
101A LYS 2.8 19.1 - - - +
102A VAL* 3.6 18.4 - - + -
103A LEU* 4.0 1.1 - - - +
108A ILE* 4.5 9.1 - - + +
202A GLY 4.3 0.4 + - - -
203A VAL* 1.3 75.8 - - - +
205A ALA* 1.3 58.5 + - - +
206A TYR* 3.4 25.5 - - + -
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Residues in contact with ALA 205 (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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58A THR* 5.7 4.5 - - - -
65A ALA* 4.0 8.3 - - + -
66A TRP 3.2 8.7 - - - +
67A LEU* 3.7 14.4 - - + +
100A MET* 3.1 2.8 - - - +
101A LYS* 2.5 57.0 + - - +
103A LEU* 4.5 3.9 - - + +
153A TYR* 3.2 18.3 - - - +
204A ALA* 1.3 72.8 - - - +
206A TYR* 1.3 60.1 + - - +
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Residues in contact with TYR 206 (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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29A TYR* 4.0 7.6 - - + -
31A ALA* 4.8 0.2 - - - +
65A ALA* 3.4 2.7 - - - +
66A TRP 2.9 27.9 + - - +
68A VAL* 3.8 17.5 - - + -
98A THR* 3.9 6.1 - - + -
99A GLU 3.6 4.5 - - - -
100A MET* 3.2 21.8 - - + -
108A ILE* 2.8 31.2 - - + +
110A ASN* 3.0 26.7 + - - -
193A TRP* 3.2 28.5 - + + -
194A GLY* 3.3 11.6 + - - -
204A ALA* 3.4 25.8 - - + -
205A ALA* 1.3 72.8 - - - +
207A ARG* 1.3 63.7 + - - +
209A ILE* 3.0 32.8 - - + -
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Residues in contact with ARG 207 (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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29A TYR* 5.2 0.4 - - - -
30A ASN* 3.9 1.4 - - - +
31A ALA* 3.3 25.5 + - + +
63A MET* 6.1 1.1 - - - +
64A PRO* 4.1 28.4 + - - +
65A ALA* 4.0 7.9 - - - +
99A GLU* 2.8 53.3 + - - +
153A TYR* 3.5 27.9 - - + +
206A TYR* 1.3 74.4 - - - +
208A ASP* 1.3 67.4 + - + +
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Residues in contact with ASP 208 (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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28A ASP* 5.0 0.2 - - - +
29A TYR* 2.7 26.9 - - - +
30A ASN* 3.0 22.2 + - - +
97A THR* 4.4 2.5 - - + -
98A THR* 3.5 2.4 - - - -
99A GLU* 2.8 49.0 + - + +
206A TYR 3.3 1.8 - - - -
207A ARG* 1.3 83.6 + - - +
209A ILE* 1.3 70.1 + - - +
210A LYS* 3.8 27.3 + - - -
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Residues in contact with ILE 209 (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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28A ASP* 2.8 30.5 - - - +
29A TYR* 3.0 19.0 + - + +
45A TRP* 4.0 22.9 - - + -
96A MET* 5.6 8.7 - - + -
97A THR 3.4 3.8 - - - -
98A THR* 3.7 17.0 - - + +
193A TRP* 3.5 41.5 - - + -
206A TYR* 3.0 39.7 - - + -
208A ASP* 1.3 78.9 + - - +
210A LYS* 1.3 65.7 + - - +
211A PHE* 6.1 0.2 - - + -
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Residues in contact with LYS 210 (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 LEU* 4.0 24.2 - - + +
27A PHE 3.6 2.5 - - - -
28A ASP* 3.4 32.2 + - + -
30A ASN* 4.5 5.9 - - - +
95A ARG 3.7 1.3 - - - +
96A MET* 3.3 7.9 - - - +
97A THR* 2.6 59.1 + - + +
208A ASP* 3.8 28.9 + - - -
209A ILE* 1.3 74.8 - - - +
211A PHE* 1.3 59.3 + - - +
212A GLU 4.2 0.2 - - - -
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Residues in contact with PHE 211 (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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25A ALA 3.5 0.5 - - - +
26A LEU* 3.3 6.4 - - - +
27A PHE* 2.7 63.6 + + + +
45A TRP* 5.4 1.8 - - + -
81A LEU* 4.2 5.8 - - + -
89A ALA* 5.7 0.2 - - + -
94A TRP* 3.6 36.1 - + + -
95A ARG 3.6 3.6 - - - -
96A MET* 3.7 24.9 - - + -
112A TYR* 3.3 52.9 - + + -
191A ILE* 4.1 19.3 - - + -
209A ILE* 6.1 0.4 - - + -
210A LYS* 1.3 75.1 - - - +
212A GLU* 1.3 61.0 + - - +
213A ILE* 3.9 22.2 - - + -
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Residues in contact with GLU 212 (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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25A ALA 3.2 12.3 - - - +
26A LEU* 4.2 14.2 - - + +
94A TRP* 2.9 29.0 - - - +
95A ARG* 3.0 37.8 + - + +
210A LYS 5.7 0.2 - - - -
211A PHE* 1.3 76.1 - - - +
213A ILE* 1.3 71.9 + - - +
214A GLN* 3.5 10.2 + - - +
270A ILE* 4.5 6.1 - - - +
766A ARG* 2.6 57.4 + - + +
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Residues in contact with ILE 213 (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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25A ALA* 2.6 43.1 + - + +
27A PHE* 3.4 25.8 - - + -
81A LEU* 4.2 6.1 - - + -
85A GLN* 3.6 38.4 - - + +
88A GLN* 3.4 37.1 + - + +
89A ALA* 3.7 22.7 - - + +
93A GLY 3.7 2.9 - - - -
94A TRP* 4.2 1.8 - - - -
211A PHE* 3.9 18.6 - - + -
212A GLU* 1.3 72.7 - - - +
214A GLN* 1.3 65.8 + - - +
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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