Contacts of the strand formed by residues 14 - 20 (chain C) in PDB entry 3KYR
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 TYR 14 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.4 12.3 - - + -
7C ARG 3.4 10.1 - - - +
13C GLY* 1.3 81.2 - - - -
15C TYR* 1.3 59.0 + - - +
30C LEU* 3.4 5.8 - - - +
31C VAL* 2.9 32.9 + - + +
154C LEU* 3.7 49.8 - - + -
155C CYS 3.0 15.9 + - - -
170C VAL* 3.6 27.4 - - + +
171C GLY 3.5 28.5 - - - -
229C SER* 4.9 6.7 + - - +
335C ALA* 4.2 13.7 - - + -
339C GLU* 2.7 29.8 + - - +
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Residues in contact with TYR 15 (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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5C ASN 3.8 0.2 - - - +
6C LEU* 3.2 11.4 - - - -
7C ARG* 2.8 68.7 + - + +
8C GLY* 3.9 11.7 + - - -
9C LYS* 6.1 0.3 - - - +
13C GLY 4.3 0.9 - - - -
14C TYR* 1.3 74.4 - - - +
16C VAL* 1.3 61.3 + - - +
17C GLU 5.0 0.2 - - - -
28C ASN* 3.3 41.1 - - + -
29C ILE 3.1 25.6 - - - +
30C LEU* 3.6 3.6 - - - +
31C VAL* 4.4 0.9 - - - +
113C SER 3.7 17.5 - - - -
114C ASN* 3.2 27.6 + - + +
115C TRP* 3.9 22.4 - + + -
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Residues in contact with VAL 16 (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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5C ASN* 3.7 30.3 - - + +
6C LEU* 3.6 14.8 - - + -
15C TYR* 1.3 74.4 - - - +
17C GLU* 1.3 73.9 + - - +
18C MET* 3.6 19.1 + - + -
28C ASN* 3.5 4.0 - - - -
29C ILE* 2.9 39.1 + - + +
31C VAL* 3.8 15.5 - - + -
87C ILE* 4.2 15.5 - - + -
89C HIS* 5.9 1.3 - - + -
119C LEU* 4.7 6.1 - - + -
174C MET* 5.1 5.8 - - - -
176C ILE* 6.0 0.7 - - + -
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Residues in contact with GLU 17 (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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5C ASN 4.4 3.6 + - - +
15C TYR* 5.0 0.2 - - - -
16C VAL* 1.3 84.7 - - - +
18C MET* 1.3 68.0 + - - +
26C THR* 3.8 29.9 + - + +
27C LEU 3.6 0.7 - - - +
28C ASN* 3.4 21.8 + - - +
50C ARG* 5.4 1.9 + - - -
87C ILE* 3.7 3.1 - - - +
88C PRO* 3.4 37.1 - - + +
89C HIS* 4.6 18.5 + - + +
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Residues in contact with MET 18 (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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16C VAL* 4.4 6.5 - - + +
17C GLU* 1.3 79.9 - - - +
19C THR* 1.3 68.4 + - - +
20C VAL* 5.5 1.8 - - + -
26C THR* 3.4 5.2 - - - +
27C LEU* 2.9 33.4 + - + -
29C ILE* 3.6 42.2 - - + -
38C PHE* 3.9 14.8 - - + -
85C VAL* 3.5 29.4 - - + -
86C SER 3.4 11.2 - - - +
87C ILE* 4.2 15.7 - - + -
88C PRO* 3.7 2.7 - - - -
119C LEU* 4.1 21.1 - - + -
136C PHE* 3.9 19.1 - - + -
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Residues in contact with THR 19 (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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18C MET* 1.3 79.4 - - - +
20C VAL* 1.3 66.0 + - - +
24C PRO* 3.6 25.8 - - + +
25C GLN 3.0 8.7 - - - +
26C THR* 3.6 21.3 - - - +
85C VAL* 3.1 6.2 - - - +
86C SER* 2.8 52.3 + - - +
88C PRO* 4.0 18.4 - - + -
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Residues in contact with VAL 20 (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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18C MET* 5.5 2.0 - - + -
19C THR* 1.3 80.3 - - - +
21C GLY* 1.3 61.6 + - - +
25C GLN* 2.7 41.2 + - + +
27C LEU* 4.2 21.5 - - + -
29C ILE* 6.4 0.2 - - + -
38C PHE* 4.2 18.6 - - + -
40C VAL* 5.0 3.1 - - + -
52C TYR* 3.3 41.3 - - + -
83C ASP* 4.6 0.2 - - - +
84C LEU 3.1 8.7 - - - +
85C VAL* 3.8 19.5 - - + -
99C ILE* 4.4 10.3 - - + -
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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