Contacts of the strand formed by residues 102 - 108 (chain C) in PDB entry 1KYZ
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 VAL 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C VAL* 4.1 20.4 - - + -
95C ARG 3.6 3.6 - - - -
96C THR* 4.3 19.1 - - + -
97C GLN* 5.5 0.2 - - - -
100C GLY 5.2 2.9 - - - +
101C LYS* 1.3 79.7 - - - +
103C GLN* 1.3 60.8 + - - +
104C ARG* 4.1 27.7 + - - +
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Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C SER* 3.6 25.8 + - - -
59C PRO* 4.9 3.8 - - + +
60C ILE* 4.0 21.6 - - - +
93C SER 4.0 0.2 - - - +
94C VAL* 3.5 4.2 - - - +
95C ARG* 2.7 77.8 + - + +
97C GLN* 2.8 29.4 + - + +
101C LYS 3.9 0.8 + - - -
102C VAL* 1.3 75.6 - - - +
104C ARG* 1.3 74.1 + - - +
105C LEU* 4.0 0.4 - - + +
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Residues in contact with ARG 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C SER* 3.6 4.5 - - - -
59C PRO* 3.3 26.8 - - - +
78C ASP* 2.6 38.8 + - - +
82C ARG* 3.9 33.4 - - - +
92C CYS* 3.8 19.3 - - - -
93C SER 3.6 2.9 - - - -
94C VAL* 4.3 14.6 - - + +
102C VAL* 4.1 32.6 + - - +
103C GLN* 1.3 77.2 - - - +
105C LEU* 1.3 63.0 + - - +
106C TYR* 3.3 29.1 + - + -
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLN* 3.7 22.5 - - + +
57C ILE* 3.6 4.0 - - - -
58C SER* 3.5 33.4 - - - +
61C GLU* 4.4 2.0 - - - +
92C CYS* 3.2 7.3 - - - -
93C SER* 2.8 54.8 + - - +
95C ARG* 3.7 53.2 - - + +
103C GLN* 4.0 1.8 - - - +
104C ARG* 1.3 75.4 - - - +
106C TYR* 1.3 62.8 + - - +
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Residues in contact with TYR 106 (chain C).
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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48C ILE* 4.0 20.4 - - + +
55C ALA 3.8 0.7 - - - +
56C GLN* 3.1 4.7 - - - -
57C ILE* 2.8 45.5 + - - +
59C PRO* 3.8 13.9 - - + -
62C ILE* 4.8 1.8 - - + -
78C ASP* 2.7 37.8 + - - -
81C LEU* 3.5 48.0 - - + -
82C ARG* 3.4 10.4 + - - +
85C ALA* 4.1 6.3 - - + -
90C LEU* 4.1 8.7 - - + -
91C THR 3.5 11.2 - - - +
92C CYS* 3.9 15.7 - - + -
104C ARG* 3.3 32.5 - - + -
105C LEU* 1.3 74.8 - - - +
107C GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ILE* 3.9 7.2 - - - -
55C ALA 3.1 19.7 - - - -
56C GLN* 4.0 2.5 - - - +
90C LEU* 3.2 12.8 - - - +
91C THR* 2.8 44.8 + - - -
106C TYR* 1.3 74.5 - - - +
108C LEU* 1.3 56.2 + - - -
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 4.0 28.7 - - + +
48C ILE* 3.7 14.7 - - + +
49C ALA* 3.9 31.2 - - + -
55C ALA 4.4 1.6 + - - -
89C ILE 4.3 1.3 - - - -
90C LEU* 4.1 17.0 - - + -
91C THR* 3.7 9.1 + - - +
107C GLY* 1.3 71.9 - - - -
109C ALA* 1.3 68.9 + - - +
110C THR* 3.7 1.4 + - - +
112C ALA* 4.6 13.0 - - + +
116C VAL* 4.1 15.5 - - + -
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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