Contacts of the strand formed by residues 381 - 390 (chain F) in PDB entry 4CDC
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 HIS 381 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228E GLN* 3.6 16.3 + - - -
234E CYS* 3.3 33.8 - - + +
349E ALA* 3.2 6.2 - - - +
350E PHE* 3.0 43.6 + + + +
352E VAL* 3.5 20.2 - - + -
379F THR* 4.7 0.6 - - - -
380F ASN* 1.3 91.3 + - - +
382F ALA* 1.3 63.9 + - - +
383F VAL* 3.6 19.0 - - + +
403F ASN* 2.9 25.7 + - - -
404F SER* 4.2 1.1 - - - -
405F TRP* 3.6 21.1 + + - -
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Residues in contact with ALA 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E CYS* 3.5 24.7 - - - +
235E TYR* 3.7 31.6 - - + +
238E ALA* 3.7 10.4 + - + +
277E GLY 5.7 0.4 - - - +
279E PRO* 4.0 16.8 - - + -
348E VAL 3.4 7.6 - - - +
349E ALA* 4.3 4.7 - - + +
381F HIS* 1.3 75.8 + - - +
383F VAL* 1.3 66.8 + - - +
404F SER* 4.9 3.3 + - - -
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Residues in contact with VAL 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E ALA* 3.7 8.2 - - - +
347E ALA* 3.4 4.9 - - - -
348E VAL* 2.8 48.7 + - + +
350E PHE* 3.8 24.9 - - + -
381F HIS* 3.6 28.5 - - + +
382F ALA* 1.3 79.3 - - - +
384F LEU* 1.3 59.8 + - - +
401F VAL* 3.2 26.0 - - + -
402F LYS 3.6 8.7 - - - +
403F ASN* 3.9 12.8 - - - +
415F PHE* 4.4 4.7 - - + -
426F ILE* 4.5 0.9 - - + -
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Residues in contact with LEU 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E VAL* 4.5 6.5 - - + -
238E ALA* 3.7 12.1 - - - +
241E GLY* 3.5 27.4 - - - +
242E MET* 3.5 29.8 - - + +
345E PRO* 4.0 17.0 - - + -
346E MET 3.5 25.8 - - - +
347E ALA 4.0 0.4 - - - +
383F VAL* 1.3 75.8 - - - +
385F LEU* 1.3 64.0 + - - +
386F VAL* 3.4 8.6 + - + +
401F VAL* 3.4 4.5 - - - -
402F LYS* 2.7 62.4 + - + +
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Residues in contact with LEU 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E MET* 4.0 21.1 - - + -
340E LEU* 3.4 17.1 - - + +
345E PRO* 3.2 27.5 - - - +
346E MET* 2.9 36.1 + - + +
348E VAL* 4.1 16.9 - - + +
383F VAL 4.0 1.4 + - - -
384F LEU* 1.3 70.7 - - - +
386F VAL* 1.3 59.9 + - - +
387F GLY 3.9 1.1 - - - +
399F TRP* 3.3 62.4 - - + -
400F ILE 3.7 10.5 - - - +
401F VAL* 4.2 7.2 - - + +
426F ILE* 5.9 1.1 - - + -
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Residues in contact with VAL 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E TRP* 4.4 0.3 - - - -
212E ASP* 3.9 10.5 - - - +
213E TRP* 3.1 33.1 + - + -
214E ARG* 4.5 2.0 - - - +
222E VAL* 4.3 20.9 - - + -
340E LEU* 4.0 7.9 - - - -
345E PRO* 4.5 5.4 - - + -
384F LEU* 3.6 25.6 - - + +
385F LEU* 1.3 79.0 - - - +
387F GLY* 1.3 60.8 + - - +
400F ILE* 2.9 34.3 + - + +
402F LYS* 4.1 15.3 - - + -
414F TYR* 3.9 17.0 - - + -
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Residues in contact with GLY 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211E TRP 3.1 13.5 - - - -
340E LEU* 3.7 14.3 - - - +
385F LEU* 3.8 1.0 - - - +
386F VAL* 1.3 81.6 - - - +
388F TYR* 1.3 63.4 + - - +
399F TRP* 3.5 12.0 - - - -
400F ILE* 2.8 37.2 + - - +
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Residues in contact with TYR 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LEU* 3.7 9.0 - - - +
208E PRO* 2.6 46.7 + - - +
209E THR 3.4 16.2 - - - -
210E SER* 3.4 6.7 - - - -
211E TRP* 2.8 42.4 + - + +
337E LYS* 3.7 35.0 - - + -
340E LEU* 3.9 16.6 - - + -
341E VAL* 3.8 22.0 - - + +
387F GLY* 1.3 75.6 - - - +
389F GLY* 1.3 59.9 + - - +
398F TYR* 3.4 19.1 - - - +
399F TRP* 3.8 7.4 - + + -
400F ILE* 4.1 5.6 - - - +
419F ARG* 3.6 21.1 - - - +
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Residues in contact with GLY 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E THR 4.6 0.4 - - - -
210E SER* 4.0 15.3 - - - -
388F TYR* 1.3 79.3 - - - +
390F THR* 1.3 61.7 + - - -
398F TYR* 2.8 48.1 + - - -
419F ARG* 3.1 14.5 + - - -
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Residues in contact with THR 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E THR* 4.4 24.2 - - + +
210E SER* 5.2 1.1 - - - -
389F GLY* 1.3 75.6 - - - -
391F ASP* 1.3 64.6 + - - +
392F SER* 3.2 5.9 + - - -
395F GLY* 3.5 18.2 + - - -
396F MET 3.5 5.4 - - - -
397F ASP* 3.1 24.6 + - - -
398F TYR* 3.3 8.6 + - - -
419F ARG* 4.7 1.1 - - - +
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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