Contacts of the helix formed by residues 515 - 526 (chain A) in PDB entry 5NV6
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 PHE 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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508A VAL* 5.2 4.5 - - + -
509A LEU* 3.5 44.0 - - + +
512A ASP* 3.3 41.5 + - + -
513A ASN 3.2 1.0 - - - -
514A ARG* 1.3 89.9 - - + +
516A SER* 1.4 52.8 + - - +
517A MET 3.4 2.2 - - - -
518A LEU* 3.7 21.1 - - + +
519A VAL* 2.8 38.2 + - - +
541A ALA* 3.7 27.4 - - + -
542A PRO 4.1 5.2 - - - -
543A THR* 3.9 15.3 - - + -
625A VAL* 5.3 2.0 - - + -
627A VAL* 3.7 29.8 - - + -
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Residues in contact with SER 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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512A ASP 4.2 1.5 + - - -
513A ASN* 3.4 14.1 + - - -
514A ARG 3.5 0.6 - - - -
515A PHE* 1.4 76.2 - - - +
517A MET* 1.4 63.3 + - - +
519A VAL* 3.6 5.6 + - - +
520A ALA* 3.1 27.4 + - - +
544A ASN* 3.0 18.5 + - - -
548A ARG* 5.6 0.3 + - - -
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Residues in contact with MET 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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516A SER* 1.4 81.1 + - - +
518A LEU* 1.3 58.3 + - - +
520A ALA* 3.7 6.6 + - - +
521A ALA* 3.1 26.9 + - - +
544A ASN* 3.1 36.0 + - - +
547A PHE* 4.1 25.7 - - + -
548A ARG* 3.6 35.7 - - + +
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Residues in contact with LEU 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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509A LEU* 3.8 23.8 - - + -
515A PHE* 3.2 18.4 + - + +
517A MET* 1.3 76.1 - - - +
519A VAL* 1.4 59.6 + - - +
521A ALA* 3.2 4.6 + - - +
522A ILE* 2.9 44.4 + - + +
539A VAL* 5.6 3.1 - - + -
541A ALA* 3.7 31.0 - - + -
542A PRO* 3.7 33.9 - - + +
543A THR 6.2 0.2 - - - -
547A PHE* 4.0 11.9 - - + -
569A LEU* 3.8 25.4 - - + -
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Residues in contact with VAL 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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506A MET* 4.1 13.0 - - + -
509A LEU* 3.8 38.8 - - + +
510A LYS* 3.8 28.9 - - + -
515A PHE 2.8 25.0 + - - +
516A SER* 4.0 5.6 - - - +
518A LEU* 1.4 70.1 - - - +
520A ALA* 1.4 62.1 + - - +
522A ILE* 3.3 9.1 + - - +
523A GLN* 3.1 24.4 + - + +
528A THR* 4.8 0.5 + - - -
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Residues in contact with ALA 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 SER 3.1 18.0 + - - +
517A MET* 3.8 8.7 - - - +
518A LEU 3.3 0.2 - - - -
519A VAL* 1.4 75.8 - - - +
521A ALA* 1.4 59.2 + - - +
523A GLN* 3.7 6.3 + - - +
524A SER* 3.0 27.6 + - - -
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Residues in contact with ALA 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 MET 3.1 18.9 + - - +
518A LEU* 3.2 7.1 + - - +
520A ALA* 1.4 75.7 - - - +
522A ILE* 1.4 57.8 + - - +
524A SER* 3.3 8.1 + - - -
525A ALA* 3.1 23.6 + - - +
547A PHE* 5.2 7.0 - - + -
565A LEU* 3.8 17.3 - - + +
569A LEU* 3.4 28.7 - - + +
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Residues in contact with ILE 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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506A MET* 3.8 18.8 - - + -
509A LEU* 5.3 3.1 - - + -
518A LEU* 2.9 32.0 + - + +
519A VAL* 3.6 7.2 - - - +
521A ALA* 1.4 75.6 - - - +
523A GLN* 1.4 55.9 + - - +
525A ALA* 3.5 1.4 + - - +
526A GLY 3.0 7.6 + - - -
527A LEU* 2.9 44.2 + - + +
528A THR* 3.5 29.3 + - - +
531A LEU* 4.0 18.8 - - + -
539A VAL* 6.3 2.0 - - + -
569A LEU* 3.9 35.0 - - + +
573A ILE* 5.1 4.3 - - + -
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Residues in contact with GLN 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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519A VAL* 3.1 17.2 + - + +
520A ALA* 4.0 6.7 - - - +
521A ALA 3.3 0.4 - - - -
522A ILE* 1.4 73.8 - - - +
524A SER* 1.4 63.0 + - - +
526A GLY* 3.2 15.1 + - - -
528A THR* 3.1 34.6 + - - +
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Residues in contact with SER 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 ALA 3.0 14.4 + - - -
521A ALA* 3.3 10.1 + - - -
523A GLN* 1.4 77.1 - - - +
525A ALA* 1.3 59.3 + - - +
526A GLY 3.6 0.3 + - - -
562A ALA* 4.9 13.0 - - - +
565A LEU* 4.0 17.3 - - - -
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Residues in contact with ALA 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 ALA 3.1 18.0 + - - +
522A ILE 3.8 4.5 - - - +
524A SER* 1.3 75.3 - - - +
526A GLY* 1.3 60.5 + - - +
527A LEU* 3.9 13.8 - - + +
562A ALA 4.9 4.7 - - - -
565A LEU* 4.6 2.0 - - + +
566A ALA* 3.8 39.3 - - - +
569A LEU* 3.8 12.3 - - + -
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Residues in contact with GLY 526 (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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522A ILE 3.0 3.6 + - - -
523A GLN* 3.2 19.6 + - - -
524A SER 3.3 1.0 + - - -
525A ALA* 1.3 79.9 - - - +
527A LEU* 1.3 62.6 + - - +
528A THR 3.5 3.5 + - - -
529A GLU* 4.1 17.8 - - - +
530A THR* 4.2 2.9 + - - -
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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