Contacts of the strand formed by residues 326 - 334 (chain A) in PDB entry 2HD5
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 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A TRP* 3.3 18.0 + - - -
324A PHE 3.8 1.0 + - - -
325A VAL* 1.3 73.4 - - - +
327A GLN* 1.3 60.2 + - - -
346A PRO* 3.3 0.5 - - - +
347A PHE* 2.8 43.6 + - - -
397A ARG* 3.3 16.4 - - - -
399A PRO* 4.0 4.2 - - - +
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Residues in contact with GLN 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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313A TRP* 3.1 66.5 - - + +
326A GLY* 1.3 73.6 - - - -
328A LEU* 1.3 69.9 + - - +
344A PHE* 3.4 26.1 + - + +
345A ASP 3.7 10.8 - - - +
346A PRO* 5.6 0.4 - - + -
347A PHE* 3.3 5.0 - - - -
395A ILE* 3.7 2.6 - - - -
396A GLN* 2.8 49.7 + - - +
397A ARG* 2.9 33.6 + - + +
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Residues in contact with LEU 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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327A GLN* 1.3 73.8 - - - +
329A LYS* 1.3 59.3 + - - +
344A PHE* 3.2 8.5 - - - +
345A ASP* 2.8 45.7 + - + +
346A PRO 5.5 0.2 - - - +
347A PHE* 3.6 21.7 - - + -
350A LEU* 4.2 13.0 - - + -
367A PHE* 3.9 33.4 - - + -
393A PHE* 3.9 31.2 - - + -
394A SER 3.6 14.1 - - - +
395A ILE* 4.2 17.0 - - + -
396A GLN* 4.5 1.8 - - - -
68B HIS* 4.2 13.0 - - - +
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Residues in contact with LYS 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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313A ASP* 3.5 37.6 - - - +
327A GLN 3.9 1.4 + - - -
328A LEU* 1.3 72.4 - - - +
330A SER* 1.3 63.0 + - - +
331A SER* 3.8 19.7 - - - +
342A THR* 3.7 14.1 - - + -
343A VAL 3.6 2.9 - - - -
344A PHE* 3.6 19.5 - - + -
392A LYS 3.6 0.9 - - - +
393A PHE* 3.2 7.4 - - - -
394A SER* 2.7 42.1 + - - +
396A GLN* 3.6 17.6 + - + +
438A SER* 3.6 32.8 + - - +
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Residues in contact with SER 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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328A LEU 4.1 0.2 - - - -
329A LYS* 1.3 75.9 - - - +
331A SER* 1.3 62.7 + - - +
332A LEU* 5.4 1.8 - - - +
341A SER 3.6 1.9 - - - +
342A THR* 3.3 5.0 - - - -
343A VAL* 2.7 53.0 + - - +
345A ASP* 5.3 2.5 - - - -
391A LYS* 2.9 35.9 + - - +
392A LYS 3.5 3.5 + - - -
393A PHE* 3.8 19.1 - - - -
4B PHE* 5.8 0.2 - - - -
64B GLU 4.8 1.1 + - - -
66B THR* 5.0 1.6 - - - -
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Residues in contact with SER 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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313A ASP* 5.2 0.2 - - - -
329A LYS* 3.8 18.5 - - - +
330A SER* 1.3 74.7 + - - +
332A LEU* 1.3 59.9 + - - +
333A THR* 4.0 3.1 + - - -
340A CYS* 3.7 17.5 - - - -
341A SER 3.6 4.5 - - - -
342A THR* 3.7 10.4 + - - -
390A ILE 3.3 2.9 - - - +
391A LYS* 3.2 4.5 - - - -
392A LYS* 2.8 45.7 + - - +
394A SER* 5.4 1.2 + - - -
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Residues in contact with LEU 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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330A SER* 5.4 1.6 - - - +
331A SER* 1.3 72.7 - - - +
333A THR* 1.3 58.9 + - - +
334A CYS 4.1 0.3 + - - -
339A TYR 3.5 1.7 - - - +
340A CYS* 3.3 1.0 - - - -
341A SER* 2.6 48.8 + - - +
373A LEU* 3.8 23.8 - - + -
379A PRO* 4.2 5.4 - - + -
380A THR 5.2 1.6 - - - +
381A CYS* 6.4 0.4 - - - -
389A CYS* 3.7 30.1 - - + -
390A ILE 3.3 1.1 - - - +
391A LYS* 3.8 14.1 - - + -
2B GLN* 4.0 7.2 - - - +
4B PHE* 3.7 22.7 - - + -
64B GLU* 3.6 32.5 - - + +
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Residues in contact with THR 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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331A SER* 4.7 2.4 + - - -
332A LEU* 1.3 73.9 + - - +
334A CYS* 1.3 71.3 + - - +
335A THR* 3.5 2.9 + - + +
338A GLY* 3.8 15.9 - - - +
339A TYR 3.2 11.7 - - - +
340A CYS* 3.4 23.0 - - + +
389A CYS* 3.2 7.3 - - - -
390A ILE* 2.8 45.2 + - - +
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Residues in contact with CYS 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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201A ZN 2.5 35.7 - - - -
332A LEU 4.1 0.8 + - - -
333A THR* 1.3 74.7 - - - +
335A THR* 1.3 60.1 + - - +
336A ASP* 3.3 23.6 - - - -
337A CYS* 3.5 8.3 - - - -
338A GLY* 2.9 28.6 + - - -
339A TYR 3.0 11.5 + - - +
381A CYS* 3.8 13.2 - - + -
387A LYS* 3.8 18.4 - - - -
389A CYS* 3.8 11.1 - - - -
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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