Contacts of the strand formed by residues 372 - 376 (chain A) in PDB entry 3E6G
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 372 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PRO* 4.8 3.6 - - + +
162A MET* 3.4 39.0 - - + -
289A ILE* 4.2 12.6 - - + -
314A SER* 3.5 16.8 - - - +
315A ILE 2.9 12.6 - - - +
316A VAL* 3.8 11.0 - - + -
349A HIS* 4.2 5.9 - - - -
350A PRO* 3.1 27.3 - - + +
367A GLY 4.4 7.4 - - - +
368A ILE* 4.4 13.9 - - + -
369A SER* 3.4 16.0 + - - +
370A ASP 3.4 0.6 - - - -
371A ALA* 1.3 78.4 - - - +
373A VAL* 1.3 87.1 + - - +
374A ARG 4.1 0.4 - - - +
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER* 3.2 2.9 - - - -
315A ILE* 2.8 63.5 + - + +
317A LEU* 4.2 5.6 - - + -
324A ALA* 4.1 14.1 - - + -
327A PHE* 3.7 19.7 - - + -
328A CYS* 3.7 25.1 - - - -
347A VAL* 4.6 2.0 - - + -
348A ASN 3.6 9.6 - - - +
349A HIS* 4.0 16.2 - - + +
350A PRO* 4.1 0.2 - - - -
371A ALA 3.8 1.0 + - - -
372A LEU* 1.3 83.9 - - - +
374A ARG* 1.3 60.1 + - - +
375A LEU* 3.9 6.7 + - + -
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Residues in contact with ARG 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASN* 2.8 36.9 + - - +
161A PRO* 3.6 19.5 - - + +
312A ILE* 3.8 25.8 - - + -
314A SER* 3.5 10.8 - - - +
338A GLU 3.1 24.5 + - - -
339A SER 4.6 1.6 + - - -
340A LEU* 3.4 29.1 - - + +
346A LEU* 5.8 0.6 - - - +
347A VAL* 3.6 6.9 - - - +
348A ASN* 2.9 66.7 + - - +
350A PRO* 4.4 1.8 - - + +
354A THR* 4.4 7.1 + - - +
373A VAL* 1.3 70.9 - - - +
375A LEU* 1.3 65.4 + - - +
376A SER* 3.7 7.5 + - - +
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 5.8 2.0 - - + -
279A LEU* 3.9 27.6 - - + -
312A ILE* 3.4 8.3 - - - +
313A VAL* 2.6 53.5 + - + +
315A ILE* 4.3 12.1 - - + -
327A PHE* 3.9 20.4 - - + -
334A PHE* 4.0 24.0 - - + -
346A LEU 3.8 2.2 - - - -
347A VAL* 3.7 24.7 - - + -
373A VAL* 3.9 3.3 + - + -
374A ARG* 1.3 74.6 - - - +
376A SER* 1.3 59.8 + - - +
377A VAL* 3.6 7.0 + - + -
389A LEU* 4.1 20.2 - - + -
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Residues in contact with SER 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 4.6 5.0 + - - -
311A GLY 3.9 3.1 - - - -
312A ILE* 4.7 5.4 - - - -
334A PHE* 4.6 0.7 - - - -
340A LEU* 3.6 15.9 - - - +
341A GLY* 3.3 25.8 + - - -
342A GLY 4.7 2.8 + - - -
344A GLU 4.4 1.0 + - - +
345A SER* 3.4 1.2 - - - -
346A LEU* 2.7 57.9 + - - +
374A ARG* 3.7 8.4 + - - +
375A LEU* 1.3 71.6 - - - +
377A VAL* 1.3 64.1 + - - +
378A GLY 3.4 0.9 + - - -
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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