Contacts of the strand formed by residues 376 - 384 (chain C) in PDB entry 4YCG
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 LEU 376 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C PRO* 3.7 25.6 - - + -
374C THR 4.6 4.3 - - - +
375C LYS* 1.3 79.8 - - - +
377C SER* 1.3 60.4 + - - +
378C PRO* 4.0 5.0 - - - +
397C GLU* 4.4 6.4 - - - +
398C GLY* 3.6 37.0 + - - +
400C SER 3.3 17.0 - - - +
401C VAL* 3.6 17.9 - - + -
402C ALA* 4.3 2.7 - - - -
349D THR* 3.9 32.3 - - + +
351D HIS* 4.0 8.1 - - + -
407D ARG* 6.2 0.2 - - - -
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Residues in contact with SER 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C TYR* 5.7 0.7 - - - -
376C LEU* 1.3 74.5 - - - +
378C PRO* 1.3 70.4 - - - +
398C GLY 4.3 2.2 - - - -
399C MET 3.4 3.5 + - - -
400C SER* 2.3 69.9 + - - -
401C VAL 4.2 5.7 + - - -
402C ALA* 4.1 13.3 - - - +
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Residues in contact with PRO 378 (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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376C LEU 4.0 1.8 - - - +
377C SER* 1.3 93.1 - - - +
379C ILE* 1.3 64.6 + - - +
394C TYR 5.3 0.7 - - - -
395C HIS* 3.6 25.8 - - + +
396C TYR 3.5 17.5 - - - +
397C GLU* 3.5 44.6 - - - +
400C SER* 4.7 0.2 + - - -
501C ZN 4.3 3.1 - - - -
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Residues in contact with ILE 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C PHE* 5.0 1.3 - - + -
326C PRO* 4.9 7.0 - - + -
329C TYR* 3.6 44.9 - - + -
330C GLU 5.3 0.7 - - - +
377C SER 4.1 0.2 + - - -
378C PRO* 1.3 79.8 - - - +
380C SER* 1.3 61.0 + - - +
381C VAL* 3.6 19.5 - - + -
394C TYR 3.7 6.5 - - - -
396C TYR* 2.9 34.3 + - - +
399C MET* 3.6 34.8 - - + -
400C SER* 4.2 12.8 - - - +
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Residues in contact with SER 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.3 30.0 + - - -
73A TYR* 4.6 3.3 - - - +
74A THR* 4.0 18.7 - - - +
326C PRO* 3.5 12.3 - - - +
379C ILE* 1.3 74.7 - - - +
381C VAL* 1.3 63.4 + - - +
392C LEU* 5.3 1.6 - - - -
393C LYS 3.5 7.9 - - - -
394C TYR* 3.2 33.2 + - - -
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Residues in contact with VAL 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 4.6 0.2 - - - -
314C PHE* 5.7 2.2 - - + -
323C ILE* 4.1 22.4 - - + -
325C ALA 3.5 8.5 - - - +
326C PRO* 4.7 2.9 - - + -
379C ILE* 3.6 27.4 - - + -
380C SER* 1.3 79.2 - - - +
382C LEU* 1.3 62.4 + - - +
383C TYR* 3.6 23.2 - - + -
391C THR 3.6 1.7 - - - +
392C LEU* 3.5 5.3 - - - +
393C LYS* 3.0 32.6 + - - +
396C TYR* 3.7 34.1 - - + -
399C MET* 4.9 3.1 - - + -
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Residues in contact with LEU 382 (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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62A PRO* 6.5 0.4 - - + -
66A MET* 4.1 22.9 - - + +
67A ILE* 4.0 34.3 - - + +
70A TYR* 4.1 5.5 - - + -
323C ILE* 3.8 1.2 - - - -
324C ILE* 2.7 59.0 + - + -
325C ALA* 2.8 32.0 + - + +
381C VAL* 1.3 72.5 - - - +
383C TYR* 1.3 55.9 - - - +
390C PRO* 4.9 1.8 - - + -
391C THR 3.3 24.9 - - - +
392C LEU* 3.8 19.9 - - + +
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Residues in contact with TYR 383 (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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87A ARG* 5.5 0.7 + - - -
251A GLU* 3.2 32.3 + - - -
322C TRP* 3.2 26.0 - + + +
323C ILE* 4.0 15.0 - - + -
324C ILE* 3.9 9.0 - - - -
381C VAL* 3.6 18.4 - - + -
382C LEU* 1.3 76.5 - - - +
384C LYS* 1.3 68.2 + - - +
385C ASP* 3.5 17.2 + - - -
390C PRO* 3.3 1.2 - - - +
391C THR* 2.4 71.9 + - + +
393C LYS* 2.8 43.9 + - + -
396C TYR* 4.0 13.8 - + - -
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Residues in contact with LYS 384 (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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62A PRO* 3.8 37.6 - - - +
251A GLU* 4.5 1.0 - - - +
255A HIS* 5.0 2.4 + - - -
321C SER 5.6 5.4 - - - +
322C TRP* 3.0 30.9 + - + +
324C ILE* 3.9 17.9 - - + -
383C TYR* 1.3 84.2 - - - +
385C ASP* 1.3 68.8 + - - +
388C GLY* 3.9 24.2 + - - +
389C VAL 3.3 3.1 - - - -
390C PRO* 4.5 6.5 - - + -
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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