Contacts of the strand formed by residues 316 - 326 (chain C) in PDB entry 3KYS
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 LYS 316 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254C LYS* 3.5 24.9 - - - +
312C CYS* 3.1 5.3 - - - -
313C SER 2.9 34.8 + - - +
314C PHE* 3.1 8.4 - - + +
315C GLY* 1.3 80.7 - - - +
317C GLN* 1.3 63.6 + - - +
318C VAL* 3.4 1.4 + - - +
58D ARG* 4.1 29.5 - - - +
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Residues in contact with GLN 317 (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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252C PRO* 4.6 12.6 - - + +
254C LYS* 4.9 1.4 - - - +
310C LYS* 3.5 37.0 - - + +
311C VAL 3.7 5.2 - - - -
312C CYS* 4.0 9.5 - - - -
315C GLY 4.3 0.6 + - - -
316C LYS* 1.3 73.9 - - - +
318C VAL* 1.3 60.7 + - - +
319C VAL 4.0 17.7 - - - +
320C GLU* 3.5 28.0 + - - +
56D HIS* 4.9 6.2 - - - +
58D ARG* 3.1 20.3 + - - -
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Residues in contact with VAL 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C VAL* 2.9 13.8 + - + +
312C CYS 4.6 0.2 - - - -
313C SER* 3.3 25.6 - - - +
316C LYS 3.9 0.2 - - - +
317C GLN* 1.3 77.5 - - - +
319C VAL* 1.3 63.3 + - + +
346C TYR* 3.4 35.2 - - + +
56D HIS 3.9 0.9 - - - +
57D VAL* 3.9 0.5 - - - -
58D ARG* 3.2 42.4 + - + +
61D SER* 4.3 15.5 - - - +
64D ASP* 3.1 29.4 - - + +
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Residues in contact with VAL 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C THR 3.9 0.6 - - - +
310C LYS* 3.2 4.3 - - - +
311C VAL* 2.8 51.1 + - + +
317C GLN* 4.0 4.5 - - - +
318C VAL* 1.3 88.1 - - + +
320C GLU* 1.3 65.3 + - - +
321C LYS 4.3 0.2 - - - -
344C P1L 3.3 33.4 - - + +
346C TYR* 3.9 23.3 - - + -
55D VAL* 4.1 3.6 - - + -
56D HIS 3.2 10.1 - - - +
57D VAL* 4.0 27.6 - - + -
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Residues in contact with GLU 320 (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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308C SER* 2.4 34.1 + - - +
309C THR 3.4 3.1 - - - +
310C LYS* 3.5 22.9 - - + +
317C GLN* 3.5 21.6 + - - +
319C VAL* 1.3 77.1 - - - +
321C LYS* 1.3 62.5 + - - +
322C VAL* 3.9 16.6 + - + +
54D ILE 3.9 0.2 - - - +
55D VAL* 3.5 2.1 - - - -
56D HIS* 2.8 60.4 + - + +
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Residues in contact with LYS 321 (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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293C VAL* 4.0 26.5 - - - +
307C CYS 3.4 5.5 - - - +
309C THR* 2.7 50.6 + - - +
320C GLU* 1.3 70.7 - - - +
322C VAL* 1.3 59.7 + - - +
323C GLU* 3.5 27.5 + - - +
341C SER* 2.9 23.6 + - - -
342C PRO 4.3 2.0 + - - +
344C P1L 3.2 42.7 + - + +
53D GLN* 3.4 30.5 - - + +
54D ILE 3.6 5.8 - - - +
55D VAL* 4.6 2.2 - - + +
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Residues in contact with VAL 322 (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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306C THR* 4.8 14.1 - - + -
307C CYS 3.5 6.3 - - - +
308C SER* 4.4 5.4 - - - +
320C GLU* 4.0 18.8 - - + +
321C LYS* 1.3 73.0 - - - +
323C GLU* 1.3 63.4 + - - +
324C THR* 5.2 4.0 - - - +
53D GLN* 4.1 0.5 - - - -
54D ILE* 2.8 49.9 + - + +
56D HIS* 3.7 32.8 - - + +
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Residues in contact with GLU 323 (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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295C SER* 5.3 0.3 + - - -
306C THR* 4.7 0.9 - - - -
307C CYS* 2.9 46.7 + - + +
309C THR* 4.7 3.1 + - - -
321C LYS* 3.5 28.7 + - - +
322C VAL* 1.3 77.2 - - - +
324C THR* 1.3 64.2 + - - +
325C GLU* 3.7 1.8 + - - +
338C ILE* 3.6 32.0 - - + +
341C SER* 3.2 21.1 + - - -
52D HIS 5.8 1.1 - - - -
53D GLN* 3.6 24.9 + - + +
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Residues in contact with THR 324 (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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304C THR* 3.8 20.0 - - + -
305C VAL 3.4 13.5 - - - +
306C THR* 4.0 9.2 + - - +
322C VAL* 5.2 5.2 - - - +
323C GLU* 1.3 72.6 - - - +
325C GLU* 1.3 62.9 + - - +
326C TYR* 3.8 22.5 - - + +
379C ARG* 3.7 36.7 + - - +
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Residues in contact with GLU 325 (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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297C TYR* 5.6 0.9 - - + -
305C VAL* 2.7 48.0 + - + +
307C CYS* 4.7 2.7 - - - +
323C GLU 3.7 2.4 + - - -
324C THR* 1.3 74.4 - - - +
326C TYR* 1.3 85.6 + - - +
336C TYR* 3.8 25.6 - - + -
337C ARG 3.4 24.8 + - - +
338C ILE* 3.6 34.7 - - + +
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Residues in contact with TYR 326 (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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303C MET 4.3 3.1 - - - -
304C THR* 3.7 32.1 - - + +
324C THR* 3.8 31.0 - - + +
325C GLU* 1.3 95.1 + - - +
327C ALA* 1.3 67.1 + - - +
328C ARG* 5.1 0.7 - - - +
335C VAL 3.9 0.3 - - - +
336C TYR* 3.4 20.5 - - - -
379C ARG* 5.3 3.1 - - - -
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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