Contacts of the helix formed by residues 352 - 368 (chain w) in PDB entry 6AH0
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 THR 352 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351w ARG* 1.3 77.1 - - - +
353w GLY* 1.3 64.9 + - - +
354w GLU 3.6 1.1 - - - +
355w GLU* 4.1 7.3 - - - +
356w ARG* 3.2 17.2 + - - +
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Residues in contact with GLY 353 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352w THR* 1.3 68.7 - - - +
354w GLU* 1.3 66.8 + - - +
356w ARG* 3.3 2.4 + - - -
357w GLU* 2.9 21.0 + - - -
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Residues in contact with GLU 354 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352w THR* 4.6 0.2 - - - +
353w GLY* 1.3 73.3 - - - +
355w GLU* 1.3 56.9 + - - +
357w GLU* 3.2 2.2 + - - +
358w GLU* 2.9 27.0 + - - -
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Residues in contact with GLU 355 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351w ARG* 5.6 1.8 - - - +
352w THR* 4.0 11.8 + - - +
353w GLY 3.2 0.4 - - - -
354w GLU* 1.3 75.3 - - - +
356w ARG* 1.3 62.0 + - - +
358w GLU* 3.1 3.0 + - - +
359w GLU* 2.9 22.0 + - - -
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Residues in contact with ARG 356 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348w LYS* 5.5 9.9 - - - +
351w ARG* 5.0 2.5 - - - +
352w THR 3.2 17.7 + - - +
353w GLY 3.8 2.5 - - - -
355w GLU* 1.3 74.4 - - - +
357w GLU* 1.3 56.0 + - - +
359w GLU* 3.5 1.6 + - - +
360w GLU* 3.0 25.8 + - - -
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Residues in contact with GLU 357 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353w GLY 2.9 13.9 + - - -
354w GLU* 3.6 3.8 - - - +
355w GLU 3.1 0.2 - - - -
356w ARG* 1.3 76.6 - - - +
358w GLU* 1.3 56.4 + - - +
360w GLU* 3.3 3.0 + - - +
361w GLU* 2.9 24.9 + - - -
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Residues in contact with GLU 358 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354w GLU 2.9 14.2 + - - -
355w GLU* 3.7 2.5 - - - +
357w GLU* 1.3 71.7 - - - +
359w GLU* 1.3 65.7 + - - +
361w GLU* 3.2 4.2 + - - +
362w GLU* 2.9 18.7 + - - -
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Residues in contact with GLU 359 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355w GLU 2.9 15.0 + - - -
356w ARG* 3.8 2.5 - - - +
358w GLU* 1.3 73.2 - - - +
360w GLU* 1.3 65.5 + - - +
362w GLU* 2.9 13.5 + - - +
363w GLN* 2.9 11.6 + - - -
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Residues in contact with GLU 360 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356w ARG 3.0 14.9 + - - -
357w GLU* 3.3 3.6 + - - +
359w GLU* 1.3 73.9 - - - +
361w GLU* 1.3 61.9 + - - +
363w GLN* 3.2 2.9 + - - +
364w ILE* 2.9 21.0 + - - -
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Residues in contact with GLU 361 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357w GLU 2.9 14.4 + - - -
358w GLU* 3.2 5.8 + - - +
360w GLU* 1.3 76.9 - - - +
362w GLU* 1.3 56.3 + - - +
364w ILE* 3.3 1.7 + - - +
365w SER* 2.9 26.3 + - - -
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Residues in contact with GLU 362 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358w GLU 2.9 9.4 + - - -
359w GLU* 2.9 10.0 + - - +
361w GLU* 1.3 73.1 - - - +
363w GLN* 1.3 65.3 + - - +
365w SER* 3.1 2.8 + - - +
366w GLU* 2.9 21.3 + - - -
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Residues in contact with GLN 363 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172w ASP* 4.9 13.1 - - - +
359w GLU 2.9 12.6 + - - -
360w GLU* 3.2 3.1 + - - +
362w GLU* 1.3 74.2 - - - +
364w ILE* 1.3 56.5 + - - +
366w GLU* 3.4 2.5 + - - +
367w SER* 3.0 24.8 + - - -
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Residues in contact with ILE 364 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360w GLU 2.9 14.1 + - - -
361w GLU* 3.6 4.0 - - - +
363w GLN* 1.3 73.0 - - - +
365w SER* 1.3 65.3 + - - +
367w SER* 2.9 12.0 + - - +
368w GLU* 2.9 12.5 + - - -
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Residues in contact with SER 365 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361w GLU 2.9 17.4 + - - -
362w GLU* 3.7 2.9 - - - +
364w ILE* 1.3 71.9 - - - +
366w GLU* 1.3 63.5 + - - +
367w SER 3.1 0.5 + - - -
368w GLU 3.2 11.7 + - - +
369w SER* 3.3 14.6 + - - -
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Residues in contact with GLU 366 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362w GLU 2.9 13.3 + - - -
363w GLN* 3.7 4.0 - - - +
365w SER* 1.3 75.5 - - - +
367w SER* 1.3 60.2 + - - +
369w SER* 3.9 9.2 + - - +
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Residues in contact with SER 367 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167w PHE* 6.1 1.0 - - - -
172w ASP* 5.7 9.0 - - - +
363w GLN 3.0 10.6 + - - -
364w ILE* 2.9 8.4 + - - +
366w GLU* 1.3 80.5 - - - +
368w GLU* 1.3 56.2 + - - +
369w SER 3.4 5.3 + - - +
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Residues in contact with GLU 368 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364w ILE 2.9 12.3 + - - -
365w SER* 3.2 5.8 + - - +
367w SER* 1.3 75.4 - - - +
369w SER* 1.3 56.7 + - - +
370w GLU 4.4 0.2 + - - -
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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