Contacts of the helix formed by residues 325 - 340 (chain A) in PDB entry 4GL5
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 HIS 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A LEU* 2.9 36.3 + - + +
322A ILE 3.5 10.8 + - - +
323A ALA 3.6 0.4 - - - -
324A LYS* 1.3 93.1 + - + +
326A PRO* 1.4 69.1 - - - +
327A ASN* 3.4 20.4 + - - +
328A VAL* 3.2 14.2 + - + +
329A GLU 3.1 17.0 + - - -
413A PHE* 3.4 45.8 + + + +
469A GLU* 5.4 4.8 + - - -
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Residues in contact with PRO 326 (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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322A ILE 4.9 0.7 - - - +
323A ALA 5.7 1.3 - - - +
324A LYS 3.9 6.1 - - - +
325A HIS* 1.4 84.9 - - - +
327A ASN* 1.3 80.8 + - - +
329A GLU* 3.2 14.3 + - + +
330A GLU* 3.0 35.8 + - - +
459A HIS* 6.5 0.4 - - + -
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Residues in contact with ASN 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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325A HIS* 3.8 17.1 + - - +
326A PRO* 1.3 92.3 - - + +
328A VAL* 1.3 85.0 + - - +
330A GLU* 3.7 11.5 + - - +
331A ALA* 3.6 16.5 + - - +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 4.9 2.7 - - + -
325A HIS* 3.2 17.8 + - + +
326A PRO 3.1 0.8 - - - -
327A ASN* 1.3 88.8 - - - +
329A GLU* 1.3 67.4 + - - +
330A GLU 3.1 1.8 - - - -
331A ALA* 3.0 20.3 + - + +
332A ILE* 3.2 22.6 + - + +
355A VAL* 6.0 0.4 - - + -
359A PHE* 3.8 32.1 - - + -
413A PHE* 4.8 9.2 - - + -
414A THR* 6.4 0.2 - - - -
415A LEU* 4.4 28.0 - - + +
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Residues in contact with GLU 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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322A ILE* 3.5 41.0 - - + +
323A ALA* 4.8 0.5 - - - -
325A HIS 3.1 9.8 + - - +
326A PRO* 3.2 16.9 + - + +
328A VAL* 1.3 79.7 - - - +
330A GLU* 1.3 64.7 + - + +
332A ILE* 4.0 9.5 - - + +
333A ILE* 3.0 33.4 + - + +
455A LEU* 5.7 4.2 - - + +
459A HIS* 3.5 34.5 + - - -
460A VAL* 4.6 6.7 + - - +
495A ARG* 2.7 30.4 + - - -
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Residues in contact with GLU 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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326A PRO* 3.0 28.5 + - + +
327A ASN* 3.8 10.3 + - - +
329A GLU* 1.3 78.8 - - + +
331A ALA* 1.3 64.9 + - - +
333A ILE* 3.3 5.5 + - - +
334A LYS* 3.1 24.8 + - - +
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Residues in contact with ALA 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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327A ASN 3.6 9.8 + - - +
328A VAL* 3.0 11.6 + - - +
330A GLU* 1.3 77.8 - - - +
332A ILE* 1.3 57.4 + - - +
334A LYS* 3.6 8.8 + - - +
335A GLU* 3.0 28.4 + - - +
355A VAL* 4.1 22.9 - - + +
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Residues in contact with ILE 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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322A ILE* 4.2 19.1 - - + -
328A VAL* 3.2 31.3 + - + +
329A GLU* 4.0 7.2 - - - +
330A GLU 3.2 0.2 - - - -
331A ALA* 1.3 74.3 - - - +
333A ILE* 1.3 60.3 + - + +
335A GLU* 3.2 8.3 + - - +
336A ILE* 2.9 51.2 + - + +
355A VAL* 4.0 18.4 - - + -
356A MET* 4.4 23.6 - - + -
359A PHE* 4.1 22.4 - - + -
451A LEU* 5.6 0.2 - - + -
455A LEU* 4.1 16.2 - - + -
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Residues in contact with ILE 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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329A GLU* 3.0 20.1 + - + +
330A GLU* 3.3 5.8 + - - +
332A ILE* 1.3 76.0 - - - +
334A LYS* 1.3 62.0 + - - +
336A ILE* 3.1 13.4 + - + +
337A GLN* 3.0 40.9 + - + +
455A LEU* 3.5 44.2 - - + +
456A ARG* 4.6 2.2 - - - +
495A ARG* 3.4 33.7 - - - +
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Residues in contact with LYS 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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330A GLU 3.1 17.0 + - - +
331A ALA* 3.7 8.5 - - - +
333A ILE* 1.3 76.4 - - - +
335A GLU* 1.3 58.5 + - - +
337A GLN* 3.0 17.9 + - + +
338A THR* 2.9 40.8 + - - +
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Residues in contact with GLU 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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331A ALA 3.0 14.7 + - - +
332A ILE* 3.4 10.9 - - - +
334A LYS* 1.3 75.1 - - - +
336A ILE* 1.3 57.2 + - + +
338A THR* 3.5 6.7 + - - -
339A VAL* 3.1 47.4 + - + +
352A LYS 4.0 3.4 - - - +
353A LEU* 3.3 15.0 - - + +
354A LYS* 3.5 13.3 + - - +
355A VAL* 2.8 46.0 + - + +
356A MET* 3.0 17.8 + - - +
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Residues in contact with ILE 336 (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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332A ILE* 2.9 39.6 + - + +
333A ILE* 3.5 20.2 - - + +
334A LYS 3.1 0.2 - - - -
335A GLU* 1.3 75.4 - - + +
337A GLN* 1.3 60.8 + - + +
340A ILE* 2.8 44.9 + - + +
341A GLY 3.2 7.2 + - - +
353A LEU* 4.4 8.3 - - + -
356A MET* 5.3 0.2 - - - -
452A VAL* 3.9 39.3 - - + +
455A LEU* 4.7 4.7 - - + -
456A ARG* 4.6 27.1 - - + +
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Residues in contact with GLN 337 (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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333A ILE* 3.0 33.3 + - - +
334A LYS* 3.0 18.5 + - + +
336A ILE* 1.3 74.8 - - + +
338A THR* 1.3 67.1 + - - +
340A ILE 3.5 0.3 + - - -
341A GLY* 3.2 30.1 + - - +
496A ASN* 5.5 4.4 + - - -
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Residues in contact with THR 338 (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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334A LYS* 2.9 32.0 + - - +
335A GLU* 3.7 9.3 - - - -
337A GLN* 1.3 72.6 - - - +
339A VAL* 1.3 67.7 + - + +
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLU* 3.1 31.3 + - + +
337A GLN 4.1 0.2 - - - -
338A THR* 1.3 85.6 - - + +
340A ILE* 1.3 71.4 + - + +
343A ARG* 3.1 21.9 + - - -
349A ASP* 4.1 14.9 - - + +
352A LYS* 3.8 47.8 - - + +
353A LEU* 4.7 6.3 - - + -
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Residues in contact with ILE 340 (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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336A ILE* 2.8 31.5 + - + +
337A GLN 4.1 0.2 - - - -
339A VAL* 1.3 89.4 - - + +
341A GLY* 1.3 61.7 + - - +
343A ARG* 3.2 43.1 + - + +
344A ASP 4.0 12.6 - - - +
345A ILE* 3.9 25.8 - - + +
349A ASP* 4.4 9.0 - - + +
353A LEU* 4.1 22.0 - - + -
452A VAL* 4.3 8.5 - - + -
456A ARG* 3.3 23.1 - - - +
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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