Contacts of the strand formed by residues 373 - 377 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B PRO* 4.4 14.1 - - + +
163B THR* 5.3 7.9 - - + +
315B THR* 4.0 22.2 - - + -
316B PHE 3.7 3.8 - - - +
317B TYR* 3.6 29.6 - - + +
350B LEU* 4.0 7.8 - - - +
351B PRO* 3.2 40.5 - - + +
352B ALA 5.1 0.2 + - - -
369B ILE* 3.8 19.7 - - + -
370B SER* 3.1 25.6 + - - +
372B THR* 1.3 77.3 - - - +
374B ILE* 1.3 72.9 + - - +
375B ARG* 4.3 2.0 - - + +
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B THR* 3.6 2.3 - - - +
316B PHE* 2.8 58.4 + - + +
318B ILE* 4.5 5.4 - - + -
325B ALA* 4.3 19.7 - - + +
328B PHE* 3.2 35.4 - - + -
329B LEU* 4.6 5.8 - - + -
349B GLU 3.4 16.4 - - - +
350B LEU* 4.5 11.9 - - + -
372B THR 4.2 6.1 - - - +
373B LEU* 1.3 82.9 - - - +
375B ARG* 1.3 61.4 + - - +
376B LEU* 3.6 25.6 - - + -
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Residues in contact with ARG 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASN* 3.3 18.1 + - - +
162B PRO* 3.6 23.1 - - + +
313B MET* 3.5 35.1 - - + +
314B VAL 3.7 3.1 - - - +
315B THR* 4.3 9.9 - - - +
339B GLU 3.4 22.8 + - - -
340B SER 4.2 3.8 + - - -
341B LEU* 3.4 38.8 - - - +
347B LEU 4.8 0.2 - - - -
348B ALA* 3.7 0.7 - - - -
349B GLU* 2.7 70.4 + - - +
351B PRO* 4.7 4.9 - - + -
373B LEU* 4.3 3.1 - - + +
374B ILE* 1.3 72.4 - - - +
376B LEU* 1.3 64.3 + - - +
377B SER* 4.3 8.9 + - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B VAL* 4.0 24.5 - - + -
280B LEU* 4.2 2.0 - - + -
312B GLY 3.3 0.5 - - - +
313B MET* 3.2 5.2 - - - -
314B VAL* 2.8 41.6 + - + +
316B PHE* 4.0 22.9 - - + -
328B PHE* 4.8 4.7 - - + -
335B PHE* 3.8 21.5 - - + -
347B LEU 3.2 6.7 - - - +
348B ALA* 3.5 29.4 - - + -
374B ILE* 3.6 19.1 - - + -
375B ARG* 1.3 78.8 - - - +
377B SER* 1.3 60.0 + - - +
378B VAL* 3.6 6.7 - - + -
390B LEU* 4.0 12.6 - - + -
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Residues in contact with SER 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B HIS* 6.0 0.5 - - - -
311B THR* 6.2 0.3 - - - +
312B GLY 3.9 5.3 - - - -
313B MET* 4.5 3.7 + - - +
340B SER 4.4 0.7 - - - -
341B LEU* 3.4 24.5 - - - +
342B GLY* 3.0 26.0 + - - -
343B GLY 5.1 0.2 + - - -
345B GLU 3.8 3.6 + - - +
346B SER* 3.4 2.3 - - - -
347B LEU* 2.9 44.2 + - - +
375B ARG* 4.3 6.8 + - - +
376B LEU* 1.3 70.5 - - - +
378B VAL* 1.3 63.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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