Contacts of the helix formed by residues 395 - 406 (chain A) in PDB entry 2X1L
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 ALA 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A ALA 3.1 17.0 + - - +
392A ALA* 4.0 8.7 - - - +
393A ALA 3.3 0.6 - - - -
394A ASP* 1.3 76.6 - - - +
396A LEU* 1.3 62.4 + - - +
397A LEU 3.6 0.7 - - - -
398A GLU* 3.8 8.1 + - - +
399A ARG* 3.4 33.4 + - + +
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Residues in contact with LEU 396 (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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392A ALA 3.6 9.6 - - - +
393A ALA* 3.4 20.0 - - + +
394A ASP 3.2 1.6 - - - -
395A ALA* 1.3 76.8 - - - +
397A LEU* 1.3 57.8 + - - +
399A ARG* 3.0 17.6 + - - +
400A VAL* 2.7 39.7 + - + +
415A ALA* 3.4 37.0 - - + +
416A ILE* 3.9 17.3 - - + +
419A VAL* 3.8 25.8 - - + -
460A ILE* 4.6 4.5 - - + -
461A ALA* 5.5 4.3 - - + +
464A LEU* 3.7 23.3 - - + -
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Residues in contact with LEU 397 (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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35A PHE* 4.9 4.9 - - + -
393A ALA 4.8 0.6 + - - -
394A ASP 4.3 6.7 + - - +
395A ALA 3.6 1.0 - - - -
396A LEU* 1.3 76.9 - - - +
398A GLU* 1.3 60.2 + - + +
400A VAL* 3.9 0.3 - - - +
401A ARG* 3.0 57.8 + - - +
460A ILE* 5.9 0.2 - - - +
464A LEU* 3.8 28.5 - - + +
489A PHE* 3.7 46.9 - - + +
492A ILE* 3.9 19.9 - - + +
493A ALA 5.9 0.9 - - - +
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Residues in contact with GLU 398 (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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394A ASP 5.3 2.2 + - - +
395A ALA* 3.8 8.3 + - - +
396A LEU 3.3 0.4 - - - -
397A LEU* 1.3 76.3 - - + +
399A ARG* 1.3 65.0 + - + +
401A ARG* 3.6 20.9 + - - +
402A GLU* 3.3 30.4 + - - +
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Residues in contact with ARG 399 (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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392A ALA 5.2 2.6 + - - -
395A ALA* 3.4 26.1 + - + +
396A LEU* 3.0 20.0 + - - +
398A GLU* 1.3 80.0 - - + +
400A VAL* 1.3 63.0 + - + +
402A GLU* 3.3 13.4 + - - +
403A HIS* 3.1 40.6 + - + +
415A ALA* 3.6 38.6 + - + +
418A SER* 5.6 4.0 - - - -
419A VAL* 5.0 4.8 - - - +
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.6 24.2 - - + -
396A LEU* 2.7 33.8 + - + +
397A LEU 4.1 2.2 - - - +
399A ARG* 1.3 70.5 - - + +
401A ARG* 1.3 65.8 + - - +
403A HIS* 3.2 8.4 + - - +
404A PHE* 2.9 37.7 + - + -
412A ALA* 3.9 26.9 - - + +
415A ALA* 5.0 2.0 - - + -
416A ILE* 4.1 20.4 - - + -
464A LEU* 4.4 14.6 - - + +
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Residues in contact with ARG 401 (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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35A PHE* 3.7 18.0 - - + -
36A LYS* 6.0 2.0 - - - +
39A ASP* 2.9 42.1 + - - +
41A TYR* 6.1 1.1 - - - -
397A LEU* 3.0 52.3 + - - +
398A GLU* 3.7 24.8 - - - +
400A VAL* 1.3 76.0 - - - +
402A GLU* 1.3 63.8 + - + +
404A PHE* 3.3 4.0 + - - +
405A ASP* 3.2 33.9 + - - +
489A PHE* 5.2 0.4 - - - +
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Residues in contact with GLU 402 (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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398A GLU* 3.3 16.6 + - - +
399A ARG* 3.6 11.9 - - - +
400A VAL 3.3 0.6 - - - -
401A ARG* 1.3 77.6 - - + +
403A HIS* 1.3 65.5 + - + +
405A ASP* 3.4 17.0 + - - +
406A VAL* 3.5 16.0 + - - +
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Residues in contact with HIS 403 (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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399A ARG* 3.1 37.4 + - + +
400A VAL* 3.2 6.3 + - - +
402A GLU* 1.3 79.2 - - + +
404A PHE* 1.3 56.1 + - - +
406A VAL* 3.3 13.0 + - - +
407A PRO 3.4 0.2 - - - -
408A ALA* 2.6 47.0 + - - +
411A LEU* 3.7 51.7 + - + +
412A ALA* 3.8 13.2 - - + -
415A ALA* 4.8 6.5 - - + +
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Residues in contact with PHE 404 (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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31A ALA* 3.4 26.9 - - + -
32A ILE* 4.1 24.5 - - + +
35A PHE* 3.6 46.2 - + + -
36A LYS* 5.6 2.5 - - - -
259A LEU* 6.0 0.3 - - - +
400A VAL* 2.9 37.6 + - + +
401A ARG 3.3 4.9 + - - +
403A HIS* 1.3 75.1 - - - +
405A ASP* 1.3 62.9 + - - +
406A VAL 3.2 0.2 - - - -
407A PRO* 3.4 17.7 - - - +
408A ALA 4.5 1.1 - - - +
409A MET* 3.8 29.6 - - + -
412A ALA* 3.8 17.3 - - + -
464A LEU 5.5 3.1 - - - -
467A PRO* 4.4 9.9 - - + -
468A VAL* 4.6 13.9 - - + -
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Residues in contact with ASP 405 (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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36A LYS* 2.8 34.7 + - - -
288A ARG* 4.6 6.8 + - - -
401A ARG* 3.2 26.7 + - - +
402A GLU* 3.7 12.4 - - - +
403A HIS 3.3 0.8 - - - -
404A PHE* 1.3 76.5 - - - +
406A VAL* 1.3 66.0 + - - +
407A PRO* 4.6 0.7 - - - +
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Residues in contact with VAL 406 (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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288A ARG* 2.8 34.5 + - - +
290A PHE* 4.8 3.1 - - + -
402A GLU 3.5 17.0 - - - +
403A HIS* 3.5 11.7 - - - +
404A PHE 3.2 0.2 - - - -
405A ASP* 1.3 77.4 - - - +
407A PRO* 1.4 78.4 - - + +
408A ALA* 3.6 11.4 - - + +
411A LEU* 6.1 0.7 - - + -
603A 2HP 3.3 26.5 - - - +
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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