Contacts of the strand formed by residues 373 - 377 (chain C) in PDB entry 3ELP
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 373 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C PRO* 4.4 14.8 - - + +
163C THR* 5.3 7.4 - - + +
315C THR* 4.0 21.8 - - + -
316C PHE 3.7 4.0 - - - +
317C TYR* 3.6 30.3 - - + +
350C LEU* 4.0 8.3 - - - +
351C PRO* 3.3 41.1 - - + +
352C ALA 5.0 0.2 + - - -
369C ILE* 3.8 20.6 - - + -
370C SER* 3.1 24.8 + - - +
372C THR* 1.3 77.3 - - - +
374C ILE* 1.3 72.8 + - - +
375C ARG* 4.3 1.3 - - + +
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Residues in contact with ILE 374 (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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315C THR* 3.6 1.7 - - - +
316C PHE* 2.8 59.9 + - + +
318C ILE* 4.5 5.4 - - + -
325C ALA* 4.3 20.2 - - + +
328C PHE* 3.2 35.0 - - + -
329C LEU* 4.6 6.3 - - + -
349C GLU 3.4 16.4 - - - +
350C LEU* 4.4 12.6 - - + -
372C THR 4.2 5.8 - - - +
373C LEU* 1.3 81.0 - - - +
375C ARG* 1.3 62.4 + - - +
376C LEU* 3.6 26.5 - - + -
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Residues in contact with ARG 375 (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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161C ASN* 3.3 18.9 + - - +
162C PRO* 3.6 23.8 - - + +
313C MET* 3.5 33.9 - - + +
314C VAL 3.7 2.9 - - - -
315C THR* 4.3 10.1 - - - +
339C GLU 3.4 22.0 + - - -
340C SER 4.2 3.6 + - - -
341C LEU* 3.4 40.1 - - - +
348C ALA* 3.7 1.0 - - - -
349C GLU* 2.7 70.7 + - - +
351C PRO* 4.7 4.7 - - + -
373C LEU* 4.3 2.9 - - + +
374C ILE* 1.3 72.5 - - - +
376C LEU* 1.3 65.1 + - - +
377C SER* 4.3 9.1 + - - +
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Residues in contact with LEU 376 (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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276C VAL* 4.0 24.2 - - + -
280C LEU* 4.1 2.7 - - + -
312C GLY 3.4 0.9 - - - +
313C MET* 3.2 5.2 - - - +
314C VAL* 2.8 42.5 + - + +
316C PHE* 3.9 21.5 - - + -
328C PHE* 4.8 4.9 - - + -
335C PHE* 3.9 22.4 - - + -
347C LEU 3.2 6.5 - - - +
348C ALA* 3.5 28.7 - - + -
374C ILE* 3.6 19.5 - - + -
375C ARG* 1.3 78.5 - - - +
377C SER* 1.3 59.3 + - - +
378C VAL* 3.6 6.7 - - + -
390C LEU* 4.0 11.9 - - + -
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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
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269C HIS* 6.1 0.7 - - - -
311C THR* 6.1 0.7 - - - +
312C GLY 3.9 4.1 - - - -
313C MET* 4.5 5.4 - - - +
340C SER 4.4 0.2 - - - -
341C LEU* 3.4 23.9 - - - +
342C GLY* 3.1 25.9 + - - -
345C GLU 3.8 3.6 + - - +
346C SER* 3.4 1.7 - - - -
347C LEU* 2.9 43.3 + - - -
375C ARG* 4.3 6.6 + - - +
376C LEU* 1.3 71.5 - - - +
378C VAL* 1.3 62.2 + - - +
379C GLY 3.5 0.2 + - - -
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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