Contacts of the strand formed by residues 80 - 87 (chain A) in PDB entry 1YKI
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 HIS 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 5.7 1.3 - - + -
22A LEU* 3.8 30.0 - - + +
27A ALA* 3.7 20.7 - - + +
30A ILE* 4.1 23.1 - - + -
50A VAL* 3.9 20.4 - - + -
51A ALA 3.4 3.8 - - - -
52A SER* 3.5 27.3 + - - -
79A SER* 1.3 103.8 + - - +
81A VAL* 1.3 59.1 + - - +
82A VAL* 5.1 0.4 - - - -
190A PRO* 3.6 0.2 - - - +
191A VAL* 2.7 39.0 + - + +
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Residues in contact with VAL 81 (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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49A ILE 3.4 3.5 - - - +
50A VAL* 3.6 0.4 - - - -
51A ALA* 2.8 45.9 + - + +
57A LYS* 4.1 11.0 - - + -
60A VAL* 4.0 18.2 - - + -
75A MET* 3.3 31.9 - - + +
78A ALA* 4.2 6.3 - - + -
80A HIS* 1.3 76.8 - - - +
82A VAL* 1.3 62.4 + - - +
83A VAL* 3.9 1.4 + - - +
188A VAL* 3.4 32.5 - - + -
189A VAL 3.7 2.5 - - - -
190A PRO* 4.0 18.2 - - + -
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Residues in contact with VAL 82 (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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30A ILE* 4.6 11.7 - - + -
34A LEU* 3.8 24.5 - - + -
48A PHE* 4.5 4.7 - - + -
49A ILE 3.3 7.0 - - - +
50A VAL* 4.3 15.5 - - + +
80A HIS 5.0 0.2 - - - +
81A VAL* 1.3 75.4 - - - +
83A VAL* 1.3 68.0 + - - +
84A PHE* 3.5 28.4 + - + -
150A PHE* 3.9 24.0 - - + -
187A VAL 3.7 1.0 - - - +
188A VAL* 3.4 3.7 - - - +
189A VAL* 2.8 43.5 + - + +
191A VAL* 4.6 2.9 - - + -
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Residues in contact with VAL 83 (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 HIS 3.6 0.9 - - - +
48A PHE* 3.3 8.3 - - - -
49A ILE* 2.7 51.8 + - + +
60A VAL* 3.9 38.8 - - + -
81A VAL 4.8 1.3 - - - +
82A VAL* 1.3 74.2 - - - +
84A PHE* 1.3 62.9 + - - +
85A CYS* 3.8 12.1 - - - -
172A LEU* 3.7 27.6 - - + -
185A SER* 3.8 17.9 - - - -
187A VAL 3.7 5.8 - - - +
188A VAL* 4.4 5.2 - - + +
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Residues in contact with PHE 84 (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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34A LEU* 3.2 31.4 - - + -
47A HIS 4.1 1.8 - - - -
48A PHE* 3.9 15.9 - + - -
82A VAL* 3.5 20.0 - - + -
83A VAL* 1.3 70.3 - - - +
85A CYS* 1.3 60.5 + - - +
143A VAL* 3.7 21.8 - - + -
146A ASN* 3.4 17.7 - - - -
147A VAL* 3.5 28.3 - - + -
150A PHE* 3.7 19.5 - + + -
185A SER* 3.8 1.9 - - - -
186A LEU* 2.9 26.9 + - - +
187A VAL 2.8 25.3 + - - +
189A VAL* 3.5 29.2 - - + -
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Residues in contact with CYS 85 (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 TRP* 3.2 10.9 - - - +
47A HIS* 2.8 46.2 + - + +
48A PHE* 5.2 0.2 - - - -
49A ILE* 4.5 9.9 - - - -
83A VAL* 3.8 20.0 - - - -
84A PHE* 1.3 77.9 - - - +
86A ALA* 1.3 59.9 + - - +
143A VAL* 3.6 6.5 - - - +
178A LEU* 3.8 28.3 - - - -
183A TYR* 4.2 14.4 - - + -
184A THR 3.2 13.0 - - - +
185A SER* 4.1 2.5 - - - -
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Residues in contact with ALA 86 (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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45A PRO 3.4 6.7 - - - +
85A CYS* 1.3 74.2 - - - +
87A LYS* 1.3 70.6 + - - +
136A ALA 5.2 0.7 - - - +
139A MET 4.3 0.7 - - - -
140A ALA* 4.1 15.3 - - + +
143A VAL* 3.7 11.4 - - + -
183A TYR* 3.2 6.1 - - - -
184A THR* 2.9 36.8 + - + +
186A LEU* 3.7 26.3 - - + +
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Residues in contact with LYS 87 (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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45A PRO* 2.9 27.5 + - + +
86A ALA* 1.3 82.7 - - - +
88A THR* 1.3 60.8 + - - +
89A ALA 3.3 17.8 + - - +
90A MET* 4.1 7.9 - - - -
91A ASP* 2.7 27.2 + - - -
94A TRP* 3.7 48.5 - - + +
136A ALA* 4.7 4.7 - - - +
139A MET* 3.3 25.6 - - + +
182A GLY 3.3 12.3 + - - +
183A TYR* 3.6 23.9 + - + -
184A THR* 5.1 1.7 - - - +
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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