Contacts of the strand formed by residues 326 - 335 (chain A) in PDB entry 3IH9
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 ARG 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ARG* 3.8 2.1 - - - -
323A GLU* 3.3 26.7 + - + -
324A GLY 3.4 7.5 + - - +
325A ASP* 1.3 90.2 - - + +
327A VAL* 1.3 64.2 + - - +
328A PHE* 3.6 36.6 - - + -
406A THR* 3.4 29.7 + - + +
408A VAL* 4.3 8.3 - - + +
438A ARG* 4.5 6.7 - - - +
440A GLU* 3.0 33.9 + - - -
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Residues in contact with VAL 327 (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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320A VAL* 3.8 24.7 - - + -
321A GLU 3.1 11.9 - - - +
322A ARG* 3.2 31.4 - - - +
326A ARG* 1.3 74.7 - - - +
328A PHE* 1.3 67.2 + - - +
329A LEU* 4.0 3.1 + - + -
350A LEU* 4.5 14.6 - - + -
394A ALA* 4.5 2.5 - - + -
404A ILE* 3.8 29.4 - - + -
406A THR 3.0 7.0 + - - +
407A VAL* 3.4 12.8 - - + +
408A VAL* 2.9 26.9 + - - +
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Residues in contact with PHE 328 (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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319A PHE* 3.7 1.9 - - - +
320A VAL* 3.3 6.8 - - - +
321A GLU* 2.6 58.0 + - + +
323A GLU* 3.2 34.5 - - + -
326A ARG* 3.6 46.2 - - + -
327A VAL* 1.3 75.8 - - - +
329A LEU* 1.3 59.7 + - - +
330A HIS* 4.0 23.5 + + + +
408A VAL* 3.9 24.7 - - + +
442A GLU* 5.9 1.6 - - - -
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Residues in contact with LEU 329 (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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317A VAL* 3.6 26.5 - - + -
319A PHE 3.8 2.9 - - - +
320A VAL* 4.3 15.3 - - + -
327A VAL* 4.0 2.9 + - + -
328A PHE* 1.3 72.4 - - - +
330A HIS* 1.3 65.4 + - - +
331A LEU* 3.6 22.0 - - + -
343A VAL* 5.3 3.4 - - + +
346A ALA* 4.4 16.4 - - + -
347A LEU* 3.5 33.4 - - + +
350A LEU* 5.5 4.9 - - + -
391A ALA* 6.2 0.4 - - + -
407A VAL* 4.9 9.4 - - + -
408A VAL 2.9 14.5 + - - +
409A LEU* 3.6 19.4 - - + +
410A ASN 3.1 21.3 + - - -
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Residues in contact with HIS 330 (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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317A VAL* 3.6 1.4 - - - -
318A ARG* 2.8 37.8 + - + +
319A PHE* 3.1 61.4 + + + +
328A PHE* 4.1 23.1 - + + -
329A LEU* 1.3 79.2 + - - +
331A LEU* 1.3 62.4 + - - +
408A VAL* 5.5 1.6 - - + -
410A ASN* 3.3 44.6 + - + +
413A ARG* 5.9 4.7 - - + -
442A GLU* 5.1 2.2 + - - -
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Residues in contact with LEU 331 (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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316A ALA 3.0 12.8 - - - +
317A VAL* 4.4 2.9 - - + -
318A ARG* 4.6 1.4 - - - +
329A LEU* 3.6 23.1 - - + -
330A HIS* 1.3 85.2 - - - +
332A GLN* 1.3 66.5 + - - +
335A ILE* 4.9 5.8 - - + -
343A VAL* 4.2 30.1 - - + -
409A LEU* 4.0 21.3 - - + -
410A ASN 3.1 14.6 + - - +
411A LEU* 3.8 18.8 - - + -
413A ARG* 3.4 15.2 - - - +
414A VAL* 3.2 22.6 + - + +
425A ILE* 4.2 16.8 - - + -
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Residues in contact with GLN 332 (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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312A LEU* 3.6 2.9 - - + +
315A THR* 3.0 37.7 + - + +
316A ALA* 2.8 15.4 + - - +
317A VAL 4.4 0.4 + - - -
318A ARG* 2.5 60.0 + - + +
331A LEU* 1.3 79.1 - - - +
333A GLY* 1.3 65.1 + - - +
335A ILE* 3.3 18.7 - - - +
413A ARG* 3.5 21.1 - - + +
414A VAL* 3.3 6.2 - - - +
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Residues in contact with GLY 333 (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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312A LEU* 4.3 10.8 - - - -
332A GLN* 1.3 82.4 - - - +
334A VAL* 1.3 60.8 + - - -
335A ILE 3.5 0.3 + - - -
413A ARG 3.6 8.3 + - - -
414A VAL* 3.4 10.7 - - - +
415A ASP* 3.1 35.7 + - - -
416A ARG 3.7 0.3 - - - +
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Residues in contact with VAL 334 (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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312A LEU* 3.8 18.0 - - - +
333A GLY* 1.3 70.5 - - - -
335A ILE* 1.3 62.0 + - - +
336A ARG* 3.4 26.5 + - + +
339A GLY 5.7 0.2 + - - -
415A ASP* 4.4 11.7 - - + +
416A ARG* 3.5 48.5 - - + +
417A ILE* 5.8 0.4 - - - -
418A ASP 6.1 0.2 - - - +
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Residues in contact with ILE 335 (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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312A LEU* 3.8 4.0 - - + -
316A ALA* 3.3 29.4 - - + +
331A LEU* 4.9 6.1 - - + -
332A GLN 3.3 25.6 - - - +
334A VAL* 1.3 69.4 - - - +
336A ARG* 1.3 64.0 + - - +
339A GLY* 4.1 1.3 - - - -
340A ALA* 3.6 21.8 - - + +
343A VAL* 5.1 2.0 - - + -
414A VAL* 3.8 25.1 - - + -
416A ARG 3.1 6.5 + - - -
417A ILE* 3.1 39.1 - - + +
418A ASP* 3.0 18.0 + - - +
425A ILE* 3.7 14.4 - - + -
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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