Contacts of the helix formed by residues 388 - 401 (chain B) in PDB entry 2AX1
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 PRO 388 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ARG 3.1 6.0 - - - +
387B ASP* 1.3 88.5 - - - +
389B THR* 1.3 63.7 + - - +
390B THR 3.5 1.1 - - - -
391B PRO* 3.6 10.0 - - + +
392B LEU* 2.9 36.6 + - + +
420B TRP* 3.6 43.5 - - + -
484B ARG* 4.6 9.0 - - + +
485B VAL* 4.5 14.4 - - + -
488B CYS* 3.8 23.1 - - + -
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B CYS* 3.5 29.6 - - + -
387B ASP* 2.6 25.8 + - - -
388B PRO* 1.3 77.8 - - - +
390B THR* 1.3 68.6 + - - +
392B LEU* 3.8 1.6 - - - +
393B ALA* 3.0 22.7 + - - +
488B CYS* 3.4 15.1 - - - -
491B LYS* 2.7 33.2 + - - +
492B LEU* 4.0 7.4 - - + +
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Residues in contact with THR 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL 3.8 8.3 - - - +
145B PHE* 4.2 18.8 - - + +
146B CYS 5.2 1.3 + - - +
386B ARG* 3.8 17.9 + - - +
387B ASP 4.6 0.6 + - - -
389B THR* 1.3 78.9 - - - +
391B PRO* 1.3 75.0 - - + +
393B ALA* 3.2 5.8 + - - +
394B ARG* 2.9 62.4 + - - +
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Residues in contact with PRO 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG* 3.8 26.7 - - - +
387B ASP 3.8 7.4 - - - +
388B PRO* 3.5 15.0 - - + +
390B THR* 1.3 95.6 - - + +
392B LEU* 1.3 57.1 + - + +
394B ARG* 3.7 4.9 + - + +
395B ALA* 3.0 26.9 + - - +
407B SER* 5.1 0.5 + - - -
408B TRP* 5.7 1.0 - - - -
411B ASN* 3.6 31.6 + - + +
420B TRP* 3.9 26.9 - - + -
425B LEU* 4.6 5.8 - - + +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.3 12.6 - - + +
31B LEU* 4.0 6.5 - - + +
388B PRO* 2.9 36.3 + - + +
389B THR 3.8 2.0 - - - +
391B PRO* 1.3 75.2 - - + +
393B ALA* 1.3 67.1 + - - +
395B ALA* 3.2 3.6 + - + +
396B ALA* 3.0 24.3 + - - +
420B TRP* 5.6 3.1 - - + +
424B ILE* 3.7 33.7 - - + -
425B LEU* 4.1 16.8 - - + -
488B CYS* 3.9 15.0 - - - -
489B LEU* 3.7 29.2 - - + -
492B LEU* 3.9 12.6 - - + -
494B VAL* 4.3 5.6 - - + -
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Residues in contact with ALA 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.2 13.1 - - + +
37B VAL* 3.7 23.6 - - + +
144B VAL* 4.0 4.5 - - + -
145B PHE* 4.1 23.6 - - - -
146B CYS* 4.2 7.2 - - + +
389B THR 3.0 16.4 + - - +
390B THR* 3.6 5.6 - - - +
392B LEU* 1.3 76.9 - - - +
394B ARG* 1.3 62.7 + - - +
396B ALA* 3.4 4.0 + - - +
397B TRP* 3.1 21.0 + - - +
492B LEU* 4.8 1.1 - - + +
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLU* 4.1 17.4 + - - +
144B VAL* 2.7 39.8 + - + +
145B PHE* 3.3 37.4 - - - -
390B THR* 2.9 35.0 + - - +
391B PRO* 4.0 4.9 - - + +
393B ALA* 1.3 75.9 - - - +
395B ALA* 1.3 59.0 + - - +
397B TRP* 3.3 2.6 + - - +
398B GLU* 2.9 39.5 + - - +
407B SER* 3.5 28.8 - - - +
411B ASN* 5.9 0.7 - - - +
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.9 11.2 - - + -
391B PRO 3.0 19.4 + - - +
392B LEU* 3.2 6.7 + - - +
394B ARG* 1.3 75.1 - - - +
396B ALA* 1.3 62.6 + - - +
398B GLU* 3.4 4.7 + - - +
399B THR* 2.8 30.3 + - - -
407B SER* 4.8 0.2 + - - -
408B TRP* 4.6 3.6 - - + -
425B LEU* 3.9 12.8 - - + -
429B PHE* 3.6 32.2 - - + -
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.9 18.8 - - + -
27B SER* 3.5 13.6 - - - -
30B LEU* 3.6 11.4 - - + +
31B LEU* 4.1 28.5 - - + -
37B VAL* 5.1 0.2 - - + -
392B LEU 3.0 12.9 + - - +
393B ALA 3.6 9.2 - - - +
395B ALA* 1.3 77.4 - - - +
397B TRP* 1.3 61.1 + - - +
399B THR* 3.2 5.7 + - - -
400B ALA* 3.0 20.3 + - - +
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Residues in contact with TRP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 3.7 22.4 - - + -
19B SER 4.1 2.7 - - - -
20B LYS 3.4 37.2 - - - -
21B LEU* 3.6 22.6 - - + +
37B VAL* 4.3 9.6 - - + -
38B TYR* 4.5 1.1 - - - -
39B ALA* 3.6 28.7 - - + -
144B VAL* 3.5 30.7 - - + +
393B ALA 3.1 14.2 + - - +
394B ARG* 3.5 8.1 - - - +
396B ALA* 1.3 76.8 - - - +
398B GLU* 1.3 63.1 + - + +
400B ALA* 3.3 1.6 + - - +
401B ARG* 2.9 57.3 + - - +
403B THR* 4.0 21.8 - - + +
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ARG* 2.9 22.3 + - - +
395B ALA 4.0 3.1 - - - +
397B TRP* 1.3 83.9 - - + +
399B THR* 1.3 59.2 + - - +
401B ARG 3.1 14.9 - - - +
403B THR* 3.5 24.5 + - - +
405B VAL* 3.3 22.9 - - + +
406B ASN* 5.8 0.2 - - - +
407B SER* 2.8 37.8 + - - -
408B TRP* 3.1 38.8 + - + +
429B PHE* 5.1 2.8 - - + -
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Residues in contact with THR 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN* 4.8 3.6 + - - +
26B LEU* 3.6 43.7 - - + +
27B SER* 3.7 4.0 - - - +
395B ALA 2.8 21.3 + - - -
396B ALA* 3.5 5.6 - - - -
398B GLU* 1.3 80.3 - - - +
400B ALA* 1.3 61.9 + - - +
401B ARG 4.7 0.9 - - - +
428B HIS* 2.8 31.3 + - - +
429B PHE* 3.5 11.2 - - - -
432B ILE* 3.9 12.6 - - + -
436B GLN* 5.4 3.8 + - - -
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.8 17.0 - - + -
22B PRO* 3.9 21.7 - - + +
24B ASN* 4.1 18.8 + - + -
27B SER* 3.4 22.9 - - - +
396B ALA 3.0 12.7 + - - +
397B TRP 4.0 0.4 - - - +
399B THR* 1.3 79.4 - - - +
401B ARG* 1.3 61.1 + - - +
402B HIS* 5.7 3.9 + - - -
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Residues in contact with ARG 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 3.0 46.1 + - - +
20B LYS* 2.9 29.7 + - - +
22B PRO* 3.6 26.5 - - + +
397B TRP* 2.9 43.0 + - + +
398B GLU 3.1 21.7 - - - +
399B THR 5.0 0.9 - - - -
400B ALA* 1.3 82.2 - - - +
402B HIS* 1.3 68.1 + - - +
403B THR* 3.2 16.1 + - + -
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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