Contacts of the helix formed by residues 330 - 339 (chain A) in PDB entry 1XI1
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 ASN 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A PRO 4.7 4.0 + - - -
283A LEU* 3.4 19.8 - - - +
284A HIS* 2.9 55.9 + - + -
328A LEU 3.7 0.4 + - - -
329A SER* 1.3 72.4 - - - +
331A VAL* 1.3 70.5 + - - +
333A LEU* 3.9 8.2 - - + +
334A GLU* 3.1 24.9 + - - +
432A PHE* 3.1 21.8 - - - -
436A TRP* 5.4 3.0 - - - -
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 3.0 6.4 - - - +
330A ASN* 1.3 88.9 - - - +
332A ASP* 1.3 61.8 + - - +
334A GLU* 3.5 7.4 + - - +
335A LEU* 3.4 22.2 + - + +
432A PHE* 4.3 14.1 - - + -
435A ALA* 3.7 19.1 - - + +
436A TRP* 3.7 44.4 - - + +
439A TYR* 3.5 39.8 - - + -
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Residues in contact with ASP 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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225A ALA 4.5 5.4 - - - +
227A ARG* 4.4 12.5 + - - +
301A THR* 4.6 7.1 - - + +
328A LEU* 4.2 22.0 - - + +
329A SER* 2.5 29.2 + - - +
331A VAL* 1.3 73.5 - - - +
333A LEU* 1.3 61.8 + - - +
335A LEU* 3.3 11.9 + - - +
336A MET* 3.0 27.7 + - - +
431A VAL 5.1 0.2 - - - +
435A ALA* 3.4 10.4 - - - +
438A ARG* 2.7 42.6 + - - +
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Residues in contact with LEU 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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284A HIS* 4.6 12.8 - - + +
286A GLN* 4.6 20.4 - - + -
288A ILE* 4.6 14.6 - - + -
328A LEU* 3.9 20.4 - - + +
329A SER 2.9 17.5 + - - +
330A ASN* 4.0 4.9 - - - +
332A ASP* 1.3 75.7 - - - +
334A GLU* 1.3 65.9 + - - +
336A MET* 3.3 25.0 + - + +
337A LYS* 3.1 42.3 + - + +
342A LEU* 5.4 0.7 - - + -
347A TYR* 4.8 15.0 - - + +
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Residues in contact with GLU 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 ASN 3.1 19.8 + - - +
331A VAL* 3.8 6.3 - - - +
332A ASP 3.3 0.2 - - - -
333A LEU* 1.3 78.3 - - - +
335A LEU* 1.3 63.0 + - + +
337A LYS* 3.6 12.6 + - - +
338A GLU* 3.5 18.9 + - - +
439A TYR* 4.0 26.4 + - + -
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A THR* 4.5 13.9 - - + +
331A VAL* 3.4 8.2 + - + +
332A ASP* 3.3 14.5 + - - +
333A LEU 3.2 0.2 - - - -
334A GLU* 1.3 75.1 - - + +
336A MET* 1.3 66.0 + - - +
338A GLU* 3.2 17.3 + - - +
339A HIS* 3.0 32.3 + - + +
435A ALA 5.7 0.2 - - - +
438A ARG* 5.8 0.7 - - + -
439A TYR* 3.6 57.7 - - + +
442A ILE* 4.1 30.7 - - + -
443A THR* 3.9 14.1 - - + -
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Residues in contact with MET 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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288A ILE* 4.5 6.7 - - + -
290A CYS* 4.4 11.0 - - - -
301A THR* 4.4 8.7 - - + +
302A ILE* 3.7 36.6 - - + -
326A LEU* 4.1 10.3 - - + -
328A LEU* 3.6 19.3 - - + -
332A ASP 3.0 16.6 + - - +
333A LEU* 3.3 25.1 + - + +
335A LEU* 1.3 77.8 - - - +
337A LYS* 1.3 55.9 + - - +
340A TYR* 2.9 40.2 + - + +
342A LEU* 3.2 40.0 - - + +
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Residues in contact with LYS 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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274A LYS* 5.6 6.3 - - - +
295A LYS* 3.5 8.3 + - - -
333A LEU* 3.1 40.9 + - + +
334A GLU* 3.9 10.3 - - - +
335A LEU 3.3 0.2 - - - -
336A MET* 1.3 76.0 - - - +
338A GLU* 1.3 57.8 - - - +
340A TYR 3.2 15.2 - - - +
342A LEU* 3.5 29.1 - - + +
347A TYR* 4.8 13.3 + - - +
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Residues in contact with GLU 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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295A LYS* 3.1 28.0 + - - +
298A TYR* 3.8 27.7 + - + +
334A GLU 3.5 9.7 + - - +
335A LEU* 3.2 17.3 + - - +
336A MET 3.2 0.4 - - - -
337A LYS* 1.3 81.0 - - - +
339A HIS* 1.3 77.7 + - + +
443A THR* 5.6 2.3 - - - +
446A GLN* 5.3 2.9 - - - +
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Residues in contact with HIS 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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294A LEU* 3.3 6.6 - - - +
295A LYS* 2.7 26.9 + - - +
298A TYR* 3.7 17.3 - + + +
299A ILE* 2.7 32.2 + - + +
301A THR* 3.7 7.5 + - - +
335A LEU* 3.0 23.9 + - + +
338A GLU* 1.3 99.4 + - - +
340A TYR* 1.3 70.0 + - + +
442A ILE* 3.9 27.8 - - + +
443A THR* 5.9 1.2 - - - +
446A GLN* 3.1 37.0 + - + +
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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