Contacts of the helix formed by residues 333 - 341 (chain A) in PDB entry 4LEY
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 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ILE* 3.0 8.3 + - - +
329A GLN* 3.3 22.4 + - - -
331A TRP 3.4 2.4 - - - -
332A LEU* 1.3 80.8 - - - +
334A THR* 1.3 62.2 + - - -
335A LYS 3.6 1.8 - - - -
336A VAL 4.3 1.6 - - - -
337A ARG* 3.5 20.6 + - - +
382C LYS 4.7 0.9 - - - -
383C THR* 3.8 6.1 - - - -
386C GLU* 3.1 15.9 - - - -
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Residues in contact with THR 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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329A GLN* 3.8 27.6 - - + +
333A GLY* 1.3 72.5 - - - -
335A LYS* 1.3 61.3 + - - +
336A VAL 3.4 0.4 - - - -
337A ARG* 3.8 5.6 - - - +
338A THR* 2.9 35.6 + - - -
386C GLU* 2.7 35.6 + - + +
387C SER* 3.6 25.2 + - - +
388C SER* 4.6 2.2 - - - +
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Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A THR* 1.3 77.9 + - - +
336A VAL* 1.3 62.0 + - + +
338A THR* 3.5 5.5 + - - -
339A ASN* 2.8 42.6 + - - +
376C ASN 4.0 14.1 + - - +
377C ASN* 3.4 28.4 - - - +
382C LYS 3.9 7.9 + - - -
384C CYS 4.7 5.3 + - - -
386C GLU* 2.7 40.6 + - + +
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 4.0 9.9 - - + -
332A LEU* 3.5 35.0 + - + +
333A GLY 4.2 1.0 + - - -
334A THR 3.4 0.2 - - - -
335A LYS* 1.3 79.0 - - + +
337A ARG* 1.3 58.9 + - - +
339A ASN* 3.3 5.0 + - - +
340A LEU* 2.9 54.7 + - + +
373A TYR* 4.2 24.9 - - + +
382C LYS* 4.5 15.3 - - + +
386C GLU* 5.0 0.2 + - - -
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Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A THR 4.0 2.8 + - - -
323A LYS 2.8 24.4 + - - -
324A GLU 4.2 1.2 - - - -
325A GLY 2.4 26.1 + - - -
326A LEU* 2.5 31.3 + - + +
328A ILE* 3.7 15.9 - - + -
329A GLN* 3.3 34.5 - - - +
333A GLY 3.5 17.7 + - - +
334A THR* 3.9 5.8 - - - +
336A VAL* 1.3 80.1 - - - +
338A THR* 1.3 61.1 + - - +
340A LEU* 3.3 4.4 + - - +
341A ARG* 3.1 50.0 + - - +
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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 THR* 2.9 24.1 + - - -
335A LYS* 3.8 7.4 - - - +
337A ARG* 1.3 77.4 - - - +
339A ASN* 1.3 64.3 + - - +
341A ARG* 3.6 5.5 + - - +
342A ARG* 3.5 50.7 + - - +
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Residues in contact with ASN 339 (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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335A LYS* 2.8 30.2 + - - +
336A VAL* 3.9 4.9 - - - +
338A THR* 1.3 77.9 - - - +
340A LEU* 1.3 63.4 + - + +
342A ARG* 3.1 45.8 + - - +
343A GLU* 3.7 12.7 + - - +
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Residues in contact with LEU 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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318A TRP* 3.2 11.4 - - - -
326A LEU* 4.4 10.5 - - + -
328A ILE* 4.2 14.4 - - + -
336A VAL* 2.9 41.0 + - + +
337A ARG* 3.3 4.7 + - - +
339A ASN* 1.3 73.3 - - + +
341A ARG* 1.3 57.7 + - - +
342A ARG 3.1 5.2 - - - -
343A GLU* 3.1 36.3 + - + +
370A THR* 4.0 28.1 + - + -
373A TYR* 3.8 42.6 - - + -
374A ILE* 4.5 7.0 - - + -
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Residues in contact with ARG 341 (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 SER* 5.0 5.4 - - - -
318A TRP* 3.5 67.6 + - + +
319A PRO 4.6 0.2 + - - -
322A THR* 2.8 44.5 + - - -
323A LYS* 3.9 32.1 - - - +
325A GLY 4.7 1.4 + - - -
326A LEU* 4.3 6.4 - - + +
337A ARG* 3.1 49.4 + - - +
338A THR* 3.6 6.3 + - - +
339A ASN 3.4 0.2 - - - -
340A LEU* 1.3 74.0 - - - +
342A ARG* 1.3 60.6 + - - +
343A GLU 3.2 1.6 - - - +
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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