Contacts of the strand formed by residues 348 - 353 (chain A) in PDB entry 1HMU
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 TYR 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A LEU* 3.7 33.7 - - + -
231A ILE* 4.3 6.7 - - + -
275A ALA* 4.0 0.7 - - - +
282A ASP* 2.7 32.0 + - - +
284A ASN* 3.9 12.1 - - + -
285A VAL* 3.4 21.4 - - + +
342A GLN* 3.6 2.9 + - - +
343A PHE* 2.8 58.9 + + + +
346A GLY 3.2 4.5 - - - +
347A ASP* 1.3 79.4 - - - +
349A VAL* 1.3 59.0 + - - +
350A GLN* 3.3 40.4 + - + +
359A ASN* 3.9 12.9 + - + -
360A VAL 3.3 20.2 - - - -
361A ARG* 4.3 3.6 - - - -
362A MET* 4.2 2.5 - - - -
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Residues in contact with VAL 349 (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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340A HIS* 3.5 32.3 - - + +
341A HIS 3.3 13.0 - - - +
342A GLN* 3.5 16.2 - - - +
343A PHE* 4.6 0.2 - - - -
348A TYR* 1.3 75.8 - - - +
350A GLN* 1.3 66.1 + - - +
359A ASN* 3.1 6.1 - - - +
360A VAL* 2.9 61.0 + - + +
362A MET* 3.9 5.8 - - + -
447A SER* 3.6 19.1 - - - +
464A PHE* 3.9 13.0 - - + -
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Residues in contact with GLN 350 (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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231A ILE* 5.5 0.2 - - - +
270A ASP 3.7 14.0 - - - +
271A SER 3.4 19.6 + - - -
274A LYS* 3.9 9.3 + - - +
275A ALA* 3.5 19.0 - - - +
339A TYR* 4.3 9.5 - - + -
340A HIS* 3.4 8.9 + - - -
341A HIS 3.0 35.5 + - - +
343A PHE* 3.5 24.8 - - + -
348A TYR* 3.3 40.1 + - + +
349A VAL* 1.3 74.9 - - - +
351A HIS* 1.3 60.4 + - - +
352A LEU* 4.0 9.4 - - + -
359A ASN* 3.2 11.7 - - - +
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Residues in contact with HIS 351 (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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339A TYR 3.6 1.8 - - - -
340A HIS* 2.7 22.0 + - - +
350A GLN* 1.3 73.6 - - - +
352A LEU* 1.3 62.1 + - - +
353A ARG* 3.2 37.4 + - + -
356A TYR* 3.4 27.4 + + - +
357A SER* 3.2 5.0 - - - -
358A PHE 2.9 41.7 + - - +
359A ASN* 3.1 6.1 + - - -
443A VAL 3.5 7.0 - - - -
464A PHE* 3.4 39.0 - + + +
465A PHE 2.7 23.4 + - - -
469A ILE* 4.7 2.2 - - + -
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Residues in contact with LEU 352 (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* 3.6 55.9 - - + +
276A ILE 5.9 1.1 - - - +
336A ILE* 4.3 25.4 - - + -
337A GLU 4.4 1.8 - - - +
338A PRO* 3.4 1.0 - - - +
339A TYR* 2.8 49.2 + - + +
350A GLN* 4.0 13.7 - - + -
351A HIS* 1.3 89.1 - - - +
353A ARG* 1.3 70.7 + - - +
356A TYR 3.8 2.2 - - - -
357A SER* 3.5 16.8 - - - +
359A ASN* 4.0 4.0 - - - +
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Residues in contact with ARG 353 (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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277A ARG* 3.4 6.9 + - - -
336A ILE* 3.5 10.4 - - - +
338A PRO* 3.8 24.6 - - - +
339A TYR 3.4 10.7 + - - +
351A HIS* 3.2 31.8 - - - +
352A LEU* 1.3 89.2 + - - +
354A PRO* 1.3 75.4 - - + +
355A ALA 3.2 1.1 - - - +
356A TYR* 2.8 58.1 + - + +
357A SER* 5.2 0.2 + - - -
443A VAL* 2.9 28.3 + - - +
444A TYR* 3.5 15.0 - - - -
465A PHE 3.5 1.2 + - - -
466A ASP* 2.8 37.9 + - - +
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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