Contacts of the strand formed by residues 380 - 386 (chain A) in PDB entry 2I69
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 GLY 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A PRO 3.9 4.5 - - - +
379A PHE* 1.3 75.4 - - - +
381A ASP* 1.3 63.1 + - - -
382A SER* 3.8 0.7 + - - -
397A TRP* 3.4 2.3 - - - +
398A HIS* 3.3 24.8 - - - -
399A LYS 3.0 32.3 + - - -
401A GLY 5.3 0.4 + - - -
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Residues in contact with ASP 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ALA* 3.9 12.8 - - - +
378A PRO* 5.0 1.0 - - - +
379A PHE 4.6 3.5 - - - +
380A GLY* 1.3 71.6 - - - -
382A SER* 1.3 64.5 + - - +
383A TYR* 6.2 1.8 - - + -
396A HIS* 3.3 29.2 + - + +
397A TRP 3.4 3.6 - - - -
398A HIS* 3.3 19.7 + - - +
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Residues in contact with SER 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A SER* 3.8 7.5 + - - -
343A VAL 3.5 14.8 - - - -
344A ALA* 4.0 7.2 - - - -
377A PRO* 4.2 7.4 - - - +
378A PRO* 3.5 37.5 + - - +
380A GLY 4.7 0.4 + - - -
381A ASP* 1.3 78.7 - - - +
383A TYR* 1.3 65.0 + - - +
384A ILE* 5.1 0.3 + - - +
396A HIS* 3.3 6.0 + - - -
397A TRP* 2.7 41.7 + - - +
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Residues in contact with TYR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A SER* 3.6 2.9 + - - -
343A VAL* 2.9 41.8 + - + +
344A ALA 4.2 3.4 - - - -
345A SER* 4.2 11.9 - - - -
346A LEU* 3.6 56.1 - - + +
381A ASP* 6.2 1.3 - - + -
382A SER* 1.3 78.1 - - - +
384A ILE* 1.3 60.4 + - - +
385A VAL* 4.3 2.9 - - + -
394A ASN* 3.0 25.8 - - - +
395A HIS 3.2 4.7 - - - +
396A HIS* 4.2 31.8 - + + -
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Residues in contact with ILE 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A PHE* 4.1 13.2 - - + -
315A PRO* 4.0 14.6 - - + -
323A VAL* 4.0 19.7 - - + -
325A LEU* 3.8 33.0 - - + -
340A ILE* 4.2 18.2 - - + -
341A SER 3.8 6.7 - - - +
342A SER* 4.5 6.3 - - - +
375A LEU* 4.5 15.9 - - + -
377A PRO* 5.7 1.8 - - + -
382A SER* 4.3 0.6 + - - +
383A TYR* 1.3 71.0 - - - +
385A VAL* 1.3 60.9 + - - +
386A VAL* 4.6 0.4 - - + -
394A ASN* 3.1 5.9 - - - +
395A HIS* 2.6 39.8 + - + +
397A TRP* 4.7 18.4 - - + -
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PRO 3.5 2.4 - - - +
340A ILE* 3.4 2.9 - - - -
341A SER* 2.9 48.8 + - - +
343A VAL* 3.6 33.9 - - + -
346A LEU* 3.9 10.3 - - + +
383A TYR* 3.7 1.1 + - + -
384A ILE* 1.3 78.4 - - - +
386A VAL* 1.3 64.3 + - - +
387A GLY 4.1 0.9 - - - +
392A GLN* 3.6 30.7 - - - +
393A ILE 3.7 3.1 - - - +
394A ASN* 3.6 17.0 - - + -
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A PHE* 3.7 41.8 - - + +
311A PHE* 4.1 21.8 - - + -
327A LEU* 3.8 16.2 - - + -
338A VAL* 4.7 3.8 - - + -
339A PRO* 3.4 8.3 - - + +
340A ILE* 3.7 27.1 - - + -
384A ILE* 4.6 0.7 - - + -
385A VAL* 1.3 77.6 - - - +
387A GLY* 1.3 60.9 - - - +
391A GLN 4.1 1.7 - - - +
392A GLN* 3.5 1.7 - - - -
393A ILE* 3.1 37.5 + - + +
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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