Contacts of the strand formed by residues 304 - 313 (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 THR 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303C MET* 1.3 72.8 - - - +
305C VAL* 1.3 61.0 + - - +
324C THR* 3.8 15.5 - - + -
325C GLU 4.1 2.0 - - - -
326C TYR* 3.7 33.2 - - + +
378C ASN* 3.7 8.0 - - - +
379C ARG* 3.0 54.6 + - - -
380C ASP* 4.2 21.2 + - - -
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Residues in contact with VAL 305 (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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201C LEU* 4.6 6.1 - - + -
297C TYR* 5.6 3.6 - - + -
303C MET* 4.2 5.2 - - + -
304C THR* 1.3 76.3 - - - +
306C THR* 1.3 59.0 + - - +
307C CYS* 3.9 12.3 - - - -
324C THR* 3.4 6.3 - - - +
325C GLU* 2.7 46.0 + - + +
336C TYR* 3.4 35.9 - - + -
376C VAL* 3.3 31.6 - - + -
377C THR 3.6 2.9 - - - +
385C LEU* 4.0 21.1 - - + -
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Residues in contact with THR 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C VAL* 1.3 72.8 + - - +
307C CYS* 1.3 68.3 + - - +
308C SER* 4.8 3.6 - - - +
322C VAL* 4.8 16.8 - - + -
323C GLU 3.8 7.4 - - - +
324C THR* 4.0 6.6 - - - +
375C VAL 3.6 0.2 - - - +
376C VAL* 3.3 2.3 - - - -
377C THR* 2.7 62.3 + - + +
379C ARG* 3.6 34.2 + - - +
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Residues in contact with CYS 307 (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* 3.9 19.1 - - - +
305C VAL* 3.9 18.6 - - - -
306C THR* 1.3 76.6 - - - +
308C SER* 1.3 59.8 + - - +
309C THR* 4.0 0.4 - - - +
321C LYS 3.4 6.1 - - - +
322C VAL* 3.5 0.2 - - - -
323C GLU* 2.9 54.5 + - + +
325C GLU* 4.7 3.8 - - - -
338C ILE* 3.8 23.3 - - + -
374C LEU* 4.6 8.1 - - + -
375C VAL 3.7 3.8 - - - -
376C VAL* 3.9 13.5 - - + +
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C THR* 4.0 5.1 - - - -
307C CYS* 1.3 73.0 - - - +
309C THR* 1.3 59.8 + - - +
310C LYS* 3.7 11.0 - - - +
320C GLU* 2.4 38.6 + - - +
321C LYS 3.8 3.4 - - - -
322C VAL* 4.4 6.3 - - - +
373C LEU 3.5 1.3 - - - +
374C LEU* 3.3 5.5 - - - +
375C VAL* 2.8 49.4 + - - +
377C THR* 5.9 1.6 - - - -
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Residues in contact with THR 309 (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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307C CYS* 5.0 1.2 + - - +
308C SER* 1.3 70.9 + - - +
310C LYS* 1.3 63.0 + - - +
311C VAL* 4.1 1.0 + - + +
319C VAL 3.9 0.7 - - - +
320C GLU* 3.4 1.0 - - - -
321C LYS* 2.7 59.2 + - - +
323C GLU* 4.7 4.2 + - - -
344C P1L 3.7 31.0 - - + +
372C ILE* 3.6 25.6 - - + -
373C LEU 3.5 2.7 - - - -
374C LEU* 3.6 20.2 - - + +
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Residues in contact with LYS 310 (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* 4.4 19.6 - - + +
255C LYS 5.7 0.2 + - - -
256C GLY 3.5 23.2 + - - -
308C SER* 3.7 15.5 - - - +
309C THR* 1.3 74.0 - - - +
311C VAL* 1.3 62.4 + - - +
312C CYS* 3.7 12.9 + - - -
317C GLN* 3.5 30.0 - - + +
319C VAL 3.2 7.4 - - - +
320C GLU* 3.5 27.1 - - + -
372C ILE* 3.3 6.0 - - - +
373C LEU* 2.8 52.4 + - + +
375C VAL* 5.6 5.2 - - + -
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Residues in contact with VAL 311 (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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309C THR* 5.3 0.7 - - + -
310C LYS* 1.3 72.5 - - - +
312C CYS* 1.3 61.5 + - - +
317C GLN* 3.7 0.5 - - - -
318C VAL* 2.9 32.2 + - + -
319C VAL* 2.8 42.1 + - + +
344C P1L 4.0 20.9 - - + -
346C TYR* 4.1 15.3 - - + -
347C MET* 3.9 34.8 - - + -
370C PHE* 4.6 5.2 - - + -
371C THR 3.7 3.6 - - - +
372C ILE* 4.2 14.6 - - + -
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Residues in contact with CYS 312 (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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250C LYS 4.4 4.3 - - - +
251C PHE* 4.8 5.4 - - - -
252C PRO* 3.6 28.0 - - - -
310C LYS* 3.8 20.6 - - - -
311C VAL* 1.3 79.2 - - - +
313C SER* 1.3 60.1 + - - +
314C PHE 4.2 0.2 - - - -
315C GLY* 4.5 0.4 - - - -
316C LYS 3.1 18.4 - - - +
317C GLN* 4.0 7.0 - - - -
318C VAL* 4.6 0.4 - - - -
346C TYR* 6.3 0.7 - - - -
369C ASN 3.7 0.3 - - - +
370C PHE* 3.4 8.8 - - - -
371C THR* 2.7 57.7 + - - +
373C LEU* 4.9 0.9 - - - -
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Residues in contact with SER 313 (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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312C CYS* 1.3 73.0 - - - +
314C PHE* 1.3 78.5 + - - +
315C GLY 3.1 0.7 - - - -
316C LYS* 2.9 20.9 + - - +
318C VAL* 3.3 7.2 - - - +
346C TYR* 3.8 8.1 - - - -
369C ASN 3.3 4.3 - - - -
370C PHE* 5.7 0.2 - - - -
58D ARG* 4.2 1.2 + - - -
64D ASP* 2.5 38.5 + - - -
68D LEU* 3.8 23.3 - - - -
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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