Contacts of the strand formed by residues 321 - 329 (chain C) in PDB entry 4YCV
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 321 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268C ARG 3.3 25.9 + - - +
269C GLY* 3.9 18.2 + - - +
270C PHE* 3.5 31.6 - - + -
271C PHE* 3.0 27.4 + - - +
319C ILE* 3.7 1.8 - - - +
320C ASP* 1.3 86.0 - - + +
322C VAL* 1.3 60.4 + - - +
348C TYR 3.5 4.0 - - - -
349C TRP* 3.4 37.2 - - + +
350C ALA 5.4 0.2 - - - +
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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
----------------------------------------------------------
270C PHE* 3.7 1.3 - - - -
271C PHE 3.4 12.6 - - - +
273C VAL* 3.6 30.1 - - + -
311C LEU* 3.6 37.0 - - + +
314C LEU* 3.8 13.7 - - + -
315C ILE* 3.9 13.7 - - + -
319C ILE* 3.5 17.0 - - + +
321C LYS* 1.3 74.4 - - - +
323C TYR* 1.3 68.7 + - - +
347C PHE* 3.2 2.6 - - - +
348C TYR* 2.9 36.7 + - + +
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Residues in contact with TYR 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ARG* 3.4 13.2 + - - -
265C LEU* 3.6 24.7 - - + -
266C ASN* 2.8 26.7 + - - -
270C PHE* 3.6 26.5 - - + -
271C PHE 3.1 13.2 + - - -
272C GLU* 3.3 48.2 + - + -
273C VAL* 3.1 30.2 + - - +
311C LEU* 4.5 3.1 - - - -
322C VAL* 1.3 77.7 - - - +
324C GLU* 1.3 62.9 + - - +
325C ILE* 4.0 30.7 - - + -
345C CYS* 4.2 2.0 - - - -
346C GLU 3.2 7.9 - - - +
347C PHE* 3.3 21.8 - - + +
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Residues in contact with GLU 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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272C GLU* 5.3 0.9 - - - -
273C VAL 3.2 17.3 - - - +
274C GLU* 3.8 7.5 - - + +
275C THR* 2.4 49.3 + - - +
277C MET* 5.2 2.1 - - - +
304C ARG* 2.8 31.6 + - - -
307C THR* 4.4 9.8 + - - +
311C LEU* 4.1 13.6 - - + +
323C TYR* 1.3 78.2 - - - +
325C ILE* 1.3 72.9 - - - +
326C GLY* 4.0 2.9 - - - +
344C SER 3.5 1.9 - - - +
345C CYS* 3.1 2.9 - - - -
346C GLU 2.9 32.4 + - - -
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Residues in contact with ILE 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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258C ILE* 4.4 15.9 - - + -
261C LEU* 4.2 22.4 - - + -
262C ARG* 3.5 59.6 + - + +
272C GLU* 5.5 1.8 - - - +
323C TYR* 4.0 16.7 - - + -
324C GLU* 1.3 80.8 - - - +
326C GLY* 1.3 59.7 + - - +
343C THR* 3.9 21.5 - - + -
344C SER 3.3 5.4 - - - +
345C CYS* 3.7 19.5 - - + -
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Residues in contact with GLY 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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277C MET* 5.2 2.7 - - - -
304C ARG* 3.8 19.0 - - - +
307C THR* 5.5 1.4 - - - +
324C GLU* 4.0 3.3 - - - +
325C ILE* 1.3 76.2 - - - +
327C LYS* 1.3 65.7 + - - -
328C VAL* 3.4 4.5 - - - +
343C THR* 4.2 5.8 - - - -
344C SER* 2.9 31.2 + - - +
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Residues in contact with LYS 327 (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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254C ARG* 5.4 4.7 - - - +
277C MET* 3.8 11.5 - - + +
304C ARG* 3.7 16.9 + - - +
326C GLY* 1.3 71.8 - - - -
328C VAL* 1.3 59.9 + - - +
329C PHE* 3.6 27.2 - - + -
341C GLU* 3.5 47.6 + - + +
342C PHE* 3.8 3.3 - - - +
343C THR* 3.5 26.3 + - + +
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Residues in contact with VAL 328 (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 ARG* 3.2 25.1 - - + +
305C ILE 3.1 31.0 - - - +
306C ALA* 3.6 8.7 - - - +
307C THR* 4.6 7.9 - - + -
326C GLY 3.4 8.3 - - - +
327C LYS* 1.3 77.6 - - - +
329C PHE* 1.3 65.2 + - - +
340C PRO 3.4 3.6 - - - +
341C GLU* 3.4 2.9 - - - -
342C PHE* 2.9 50.0 + - + +
344C SER* 3.2 30.3 - - - +
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Residues in contact with PHE 329 (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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277C MET* 4.1 17.0 - - + -
288C ARG 5.1 1.0 - - - +
289C PRO* 5.4 0.7 - - - +
290C PHE* 3.4 29.2 + + + -
303C LEU* 3.5 53.3 - - + +
304C ARG* 3.2 21.4 + - + +
305C ILE* 3.8 6.8 - - - +
327C LYS* 3.6 26.7 - - + -
328C VAL* 1.3 81.3 - - - +
330C ARG* 1.3 68.5 + - - +
340C PRO 3.2 3.8 - - - -
341C GLU* 3.9 32.8 - - + -
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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