Contacts of the helix formed by residues 515 - 526 (chain A) in PDB entry 2CXN
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 VAL 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A GLU* 4.1 16.6 - - - +
512A GLN* 3.4 26.2 - - + +
514A GLY* 1.3 80.0 - - - +
516A GLU* 1.3 67.1 + - + +
517A LEU 3.5 1.1 - - - -
518A GLY* 3.9 3.6 + - - -
519A LYS* 3.5 45.0 + - - +
388B GLN 3.6 23.3 - - - +
389B HIS* 5.3 1.8 - - - +
392B TYR* 5.7 1.1 - - + -
393B GLN* 4.6 14.6 - - + +
396B HIS* 5.6 0.9 - - - -
432B GLN* 5.3 2.3 + - - +
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Residues in contact with GLU 516 (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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513A TRP* 3.3 36.6 + - + +
514A GLY 3.4 0.2 - - - -
515A VAL* 1.3 79.9 - - + +
517A LEU* 1.3 65.7 + - - +
519A LYS* 3.1 13.0 + - + +
520A GLN* 3.1 35.9 + - + +
440B LYS* 3.3 21.5 + - - -
448B GLU* 3.8 7.8 - - - +
466B LYS* 4.3 12.7 + - - +
468B PHE* 4.7 3.1 - - + -
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Residues in contact with LEU 517 (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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515A VAL 3.5 0.4 - - - -
516A GLU* 1.3 78.1 - - - +
518A GLY* 1.3 62.5 + - - +
520A GLN* 3.2 13.0 + - + +
521A LEU* 3.0 41.7 + - + +
396B HIS* 5.6 0.2 - - + -
435B ALA* 3.7 26.0 - - + +
438B LYS* 5.6 1.8 - - - +
439B GLY* 3.4 42.8 - - - +
440B LYS* 3.9 20.2 - - + -
468B PHE* 3.7 37.2 - - + -
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Residues in contact with GLY 518 (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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514A GLY 5.5 0.4 + - - -
515A VAL 3.9 5.3 + - - -
516A GLU 3.3 0.4 - - - -
517A LEU* 1.3 78.6 - - - +
519A LYS* 1.3 61.3 + - - +
521A LEU 3.5 0.2 + - - -
522A ALA* 3.1 25.9 + - - +
396B HIS* 5.3 3.8 + - - -
428B ASN* 4.8 1.6 - - - +
431B ALA* 3.7 8.6 - - - +
432B GLN* 3.4 31.5 + - - -
435B ALA* 4.3 11.9 - - - +
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Residues in contact with LYS 519 (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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215A THR* 5.4 8.1 + - - +
515A VAL* 3.5 38.4 + - - +
516A GLU* 3.1 11.5 + - + +
518A GLY* 1.3 74.1 - - - +
520A GLN* 1.3 65.8 + - + +
522A ALA* 3.4 5.3 + - - +
523A LYS* 3.2 28.9 + - + +
388B GLN* 6.0 1.8 - - - +
389B HIS* 4.6 21.8 + - + -
428B ASN* 5.5 3.6 - - - +
432B GLN* 4.7 0.4 - - - +
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Residues in contact with GLN 520 (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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516A GLU* 3.1 27.3 + - + +
517A LEU* 3.5 17.6 - - + +
519A LYS* 1.3 77.2 - - + +
521A LEU* 1.3 66.7 + - + +
523A LYS* 3.3 16.9 + - - +
524A LYS* 3.4 22.6 + - - +
440B LYS* 2.8 29.3 + - - +
448B GLU* 2.9 29.7 + - - -
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Residues in contact with LEU 521 (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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517A LEU* 3.0 33.4 + - + +
520A GLN* 1.3 77.8 - - + +
522A ALA* 1.3 62.5 + - - +
524A LYS* 3.3 35.6 + - + +
525A ILE* 3.2 26.2 + - - +
538A HIS* 6.4 0.9 - - + -
431B ALA* 3.6 15.0 - - + +
434B GLU* 3.7 25.7 - - + +
435B ALA* 3.6 39.5 - - + +
438B LYS* 4.3 17.5 - - - +
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Residues in contact with ALA 522 (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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216A GLN* 5.6 3.6 - - - +
518A GLY 3.1 18.6 + - - +
519A LYS* 3.8 6.1 - - - +
521A LEU* 1.3 74.6 - - - +
523A LYS* 1.3 64.8 + - + +
525A ILE 3.2 0.6 + - - +
526A GLU* 3.0 30.7 + - - +
427B ALA* 3.7 15.2 - - + +
428B ASN* 3.9 26.2 - - - +
431B ALA* 3.3 15.1 - - + +
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Residues in contact with LYS 523 (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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216A GLN* 3.6 34.5 - - - +
519A LYS* 3.2 16.9 + - + +
520A GLN* 3.6 11.2 - - - +
521A LEU 3.3 0.4 - - - -
522A ALA* 1.3 74.8 - - + +
524A LYS* 1.3 61.7 + - + +
526A GLU* 3.6 15.1 + - - +
527A PRO* 3.4 18.5 - - - +
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Residues in contact with LYS 524 (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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520A GLN* 3.4 15.5 + - - +
521A LEU* 3.3 39.2 + - + +
522A ALA 3.2 0.6 - - - -
523A LYS* 1.3 80.5 - - + +
525A ILE* 1.3 61.3 + - + +
527A PRO* 3.5 12.3 - - - +
528A GLU* 3.5 18.7 - - - +
538A HIS* 5.2 7.9 - - + -
438B LYS* 5.6 2.8 - - - +
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Residues in contact with ILE 525 (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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521A LEU 3.2 16.1 + - - +
522A ALA 3.2 4.0 + - - +
524A LYS* 1.3 77.2 - - - +
526A GLU* 1.3 67.4 + - - +
528A GLU* 2.9 21.4 + - - +
529A LEU* 3.4 12.0 + - + +
538A HIS* 3.6 25.1 - - + +
542A THR* 4.2 6.3 - - + -
546A ILE* 4.5 6.5 - - + -
427B ALA* 3.9 13.9 - - + +
430B LEU* 3.8 32.5 - - + -
431B ALA* 3.7 25.4 - - + +
434B GLU* 3.5 22.2 - - - +
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Residues in contact with GLU 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLN* 2.8 36.4 + - - +
522A ALA* 3.0 17.2 + - + +
523A LYS* 3.6 22.5 + - - +
525A ILE* 1.3 77.2 - - - +
527A PRO* 1.3 69.3 - - + +
529A LEU* 3.4 16.7 + - - +
530A GLU* 4.1 1.4 + - - +
420B LEU* 5.2 0.9 - - - +
423B LYS* 3.7 39.9 + - + +
424B ILE* 3.6 18.5 - - + +
427B ALA* 3.7 17.2 - - + +
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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