Contacts of the helix formed by residues 317 - 327 (chain A) in PDB entry 1A8H
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 ARG 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ASP 3.0 24.0 + - - -
84A LEU* 2.8 29.2 + - - +
85A LEU* 3.6 12.8 - - - +
86A GLY* 3.3 16.2 - - - +
312A LEU* 3.7 21.6 - - + +
316A GLY* 1.3 70.8 - - - -
318A ASP* 1.3 77.6 + - - +
320A LEU* 3.3 3.7 + - - +
321A ARG* 3.0 46.0 + - - +
457A PRO* 5.9 3.6 - - - -
458A ASP* 2.4 35.2 + - - -
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Residues in contact with ASP 318 (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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316A GLY* 3.3 0.9 - - - -
317A ARG* 1.3 92.2 + - - +
319A ALA* 1.3 62.2 + - - +
321A ARG* 3.6 6.1 + - - +
322A TYR* 3.1 23.7 + - - +
456A MET* 3.5 28.3 - - + +
457A PRO* 4.0 1.7 - - - +
458A ASP* 3.6 19.7 + - - +
459A LYS* 2.9 57.4 + - + +
497A PHE* 4.7 2.2 - - + -
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TYR* 3.6 26.2 + - + +
316A GLY 3.3 3.4 + - - +
317A ARG 3.3 0.6 - - - -
318A ASP* 1.3 76.4 - - - +
320A LEU* 1.3 66.2 + - - +
322A TYR* 3.5 3.1 + - - +
323A TYR* 3.0 24.9 + - - +
341A LEU* 4.6 5.5 - - + +
345A TYR* 3.6 33.9 - - + -
349A LEU* 3.9 14.2 - - + +
497A PHE* 5.2 1.9 - - + -
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Residues in contact with LEU 320 (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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20A LEU* 5.6 1.3 - - + -
23A ALA* 6.3 0.2 - - + -
85A LEU* 4.2 19.1 - - + -
308A PRO* 3.1 42.8 - - + +
311A LEU* 4.7 8.1 - - + +
312A LEU* 3.7 18.6 - - + +
315A TYR* 5.4 0.2 - - - +
316A GLY 3.3 8.7 + - - +
317A ARG* 3.3 9.6 + - - +
319A ALA* 1.3 80.4 - - - +
321A ARG* 1.3 63.2 + - - +
323A TYR* 3.3 3.0 + - + +
324A LEU* 3.1 46.4 + - + +
341A LEU* 4.1 23.5 - - + +
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.2 26.6 + - + +
30A ASP* 2.8 33.9 + - - +
31A PHE* 4.5 4.8 - - - +
34A ARG* 3.9 3.4 - - - +
85A LEU* 2.8 40.6 + - + +
86A GLY 3.4 6.6 + - - -
87A ILE* 3.7 9.5 - - - +
317A ARG* 3.0 29.5 + - + +
318A ASP* 3.9 3.8 - - - +
320A LEU* 1.3 76.1 - - - +
322A TYR* 1.3 63.6 + - - +
324A LEU* 3.3 3.9 + - - +
325A LEU* 3.0 31.3 + - + +
454A PRO 2.9 26.7 + - - -
455A ALA* 2.8 25.0 + - - +
457A PRO* 4.0 11.2 - - - +
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Residues in contact with TYR 322 (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 ASP 3.1 16.0 + - - +
319A ALA 3.7 4.3 - - - +
320A LEU 3.3 0.2 - - - -
321A ARG* 1.3 79.5 - - - +
323A TYR* 1.3 59.6 + - + +
325A LEU* 3.2 6.1 + - - +
326A ARG* 2.8 54.0 + - + +
344A ARG* 3.4 31.0 - - + -
348A ASP* 2.7 29.9 + - + -
349A LEU* 4.2 17.5 - - + -
404A LEU* 4.4 13.5 - - + -
408A MET* 3.2 35.7 - - + +
452A LEU* 4.5 7.2 - - + -
455A ALA* 4.6 6.1 + - + -
456A MET* 3.9 29.2 - - + -
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Residues in contact with TYR 323 (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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311A LEU* 6.1 2.0 - - + -
319A ALA 3.0 17.3 + - - +
320A LEU* 3.6 3.6 - - + +
322A TYR* 1.3 83.3 - - + +
324A LEU* 1.3 80.2 + - + +
327A GLU* 2.9 66.5 + - + +
328A ILE* 5.3 1.5 - - + +
335A PRO 4.2 2.3 + - - -
336A VAL* 3.3 36.8 - - + +
337A SER 3.3 16.8 + - - -
340A ALA* 3.5 28.9 - - + +
341A LEU* 3.8 36.8 - - + -
344A ARG* 4.7 10.5 - - + -
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.3 16.6 - - + -
23A ALA* 5.5 2.9 - - + -
24A TYR* 3.6 29.4 - - + +
27A VAL* 5.0 13.2 - - + -
85A LEU* 5.9 0.4 - - + -
290A LEU* 4.0 15.0 - - + -
308A PRO* 5.8 0.2 - - + -
320A LEU* 3.1 42.1 + - + +
321A ARG* 3.9 6.5 - - - +
323A TYR* 1.3 90.7 - - + +
325A LEU* 1.3 60.9 + - + +
328A ILE* 3.4 49.5 - - + +
336A VAL* 4.7 2.9 - - + -
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Residues in contact with LEU 325 (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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24A TYR* 5.6 0.4 - - + -
27A VAL* 4.2 16.8 - - + -
28A VAL* 4.1 28.3 - - + -
31A PHE* 4.0 29.6 - - + -
321A ARG* 3.0 22.2 + - + +
324A LEU* 1.3 77.0 - - + +
326A ARG* 1.3 62.2 + - - +
328A ILE 4.3 5.2 - - - +
400A PHE* 3.6 19.4 - - + +
401A HIS* 3.3 26.0 + - - +
404A LEU* 3.6 15.7 - - + -
454A PRO 5.2 0.2 - - - +
455A ALA* 3.9 31.6 - - + -
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Residues in contact with ARG 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A TYR* 2.8 46.3 + - + +
323A TYR* 4.5 0.7 - - - +
325A LEU* 1.3 77.6 - - - +
327A GLU* 1.3 60.4 + - - +
328A ILE 3.7 0.2 - - - -
344A ARG* 2.7 48.9 - - - +
348A ASP* 4.5 0.8 + - - -
401A HIS* 3.2 37.1 + - - +
404A LEU* 4.1 10.8 - - + -
405A GLU* 3.6 44.9 - - - +
408A MET* 5.3 2.6 - - - +
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Residues in contact with GLU 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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323A TYR* 2.9 48.9 + - + +
326A ARG* 1.3 80.8 + - - +
328A ILE* 1.3 61.8 + - + +
329A PRO* 3.5 9.7 - - - +
334A THR* 4.2 6.9 - - - +
335A PRO 6.0 1.3 - - - +
340A ALA* 4.2 11.3 - - + +
343A THR* 6.1 0.2 - - - +
344A ARG* 2.6 46.9 + - - -
401A HIS* 5.2 0.7 - - - -
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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