Contacts of the helix formed by residues 367 - 377 (chain B) in PDB entry 1AHF
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 LYS 367 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B LEU 4.0 10.1 + - - -
366B THR* 1.3 76.3 - - - +
368B GLU* 1.3 68.7 + - - +
370B VAL* 3.3 5.9 + - - +
371B LEU* 3.1 28.5 + - - +
383B ALA* 3.0 46.7 + - + +
384B SER* 4.0 12.9 + - - +
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B THR* 3.1 16.3 + - - +
367B LYS* 1.3 88.8 + - + +
369B GLN* 1.3 65.2 + - + +
371B LEU* 3.5 14.3 - - + +
372B ARG* 3.0 24.4 + - - +
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Residues in contact with GLN 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B ARG* 4.2 9.5 + - - +
364B GLY 4.3 2.1 - - - +
365B LEU* 3.6 20.6 - - + +
366B THR* 3.0 44.0 + - - +
368B GLU* 1.3 77.5 - - + +
370B VAL* 1.3 63.0 + - - +
372B ARG* 3.4 6.8 - - - +
373B LEU* 3.0 28.0 + - - +
408B VAL* 2.7 41.9 + - + +
409B LEU* 3.4 23.6 + - - +
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 4.0 12.6 - - + -
366B THR 3.0 18.5 + - - +
367B LYS 3.8 5.2 - - - +
369B GLN* 1.3 76.8 - - - +
371B LEU* 1.3 65.4 + - - +
373B LEU* 3.4 10.4 - - + +
374B ARG* 3.1 30.6 + - - +
379B VAL 4.6 1.0 - - - +
381B ALA* 3.9 24.2 + - + +
382B VAL 3.7 15.5 - - - +
383B ALA* 3.7 18.8 - - + +
385B GLY* 3.9 27.8 - - - -
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B LYS 3.1 13.6 + - - +
368B GLU* 3.5 17.7 - - + +
370B VAL* 1.3 78.1 - - - +
372B ARG* 1.3 64.2 + - - +
374B ARG* 3.1 34.3 + - - +
375B GLU* 3.0 32.1 + - + +
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Residues in contact with ARG 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B GLU 3.0 14.3 + - - +
369B GLN* 3.4 7.2 - - - +
371B LEU* 1.3 82.9 - - - +
373B LEU* 1.3 52.9 + - - +
375B GLU* 5.1 2.2 - - - -
376B GLU* 2.3 85.7 + - - +
377B PHE* 3.9 8.5 - - + -
407B ALA 3.3 24.2 + - - -
408B VAL* 3.3 22.2 - - + +
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 3.6 30.3 - - + -
369B GLN 3.0 11.6 + - - +
370B VAL* 3.4 14.8 - - + +
372B ARG* 1.3 78.1 - - - +
374B ARG* 1.3 59.8 + - - +
377B PHE* 2.7 29.0 + - + +
378B GLY 2.9 6.4 + - - -
379B VAL* 3.3 28.9 + - + +
381B ALA* 5.5 6.1 - - + +
387B VAL* 6.4 0.7 - - + -
403B ALA* 3.4 46.7 - - + +
404B ILE* 3.9 11.0 - - + +
408B VAL* 3.7 16.4 - - + -
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Residues in contact with ARG 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 4.5 10.7 - - - +
23B LEU* 4.1 22.8 - - - +
29B ARG* 3.2 7.3 + - - +
370B VAL* 3.1 16.1 + - - +
371B LEU* 3.1 42.4 + - - +
373B LEU* 1.3 79.1 - - - +
375B GLU* 1.3 66.0 + - - +
378B GLY* 2.7 28.9 + - - -
379B VAL 3.2 16.1 + - - +
380B TYR* 3.5 43.2 - - + +
381B ALA 5.2 5.2 + - - +
383B ALA* 6.1 1.6 - - - +
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Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 2.7 27.7 + - - +
371B LEU* 3.0 23.6 + - + +
372B ARG* 4.4 1.8 - - - +
374B ARG* 1.3 82.9 - - + +
376B GLU* 1.3 64.7 + - + +
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 3.8 5.2 + - - -
372B ARG* 2.3 59.5 + - + +
375B GLU* 1.3 89.5 - - + +
377B PHE* 1.3 82.4 + - + +
378B GLY 3.7 0.2 - - - -
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Residues in contact with PHE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 4.3 4.2 - - - -
31B GLY 5.0 5.9 - - - +
32B LYS* 5.4 0.2 - - - -
33B ILE* 5.8 0.2 - - - +
372B ARG* 3.9 3.4 - - + -
373B LEU* 2.7 27.4 + - + +
376B GLU* 1.3 110.6 - - + +
378B GLY* 1.3 61.0 + - - +
379B VAL* 3.4 7.2 + - + +
403B ALA* 3.2 33.7 - - + -
407B ALA* 3.6 28.5 - - + -
408B VAL* 3.6 22.9 - - + -
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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