Contacts of the strand formed by residues 518 - 523 (chain A) in PDB entry 6N8P
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 TYR 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A LEU* 3.8 1.1 - - - +
513A CYS* 3.1 27.9 + - + -
516A SER* 3.1 34.5 + - - +
517A GLY* 1.3 76.5 - - - +
519A LEU* 1.3 60.0 + - - +
530A VAL* 4.8 2.9 - - + -
531A LEU 3.5 12.6 - - - +
532A GLU* 3.9 32.8 + - + -
580A PHE* 4.0 23.1 - + - -
596A LEU* 3.7 23.5 - - + +
598A SER* 4.4 21.1 - - - +
601A ARG* 4.5 19.3 + - - -
616A HIS* 4.5 17.5 - + - -
617A GLN* 4.9 5.4 + - - -
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Residues in contact with LEU 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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439A LEU* 4.1 12.8 - - + -
447A VAL* 5.2 1.8 - - + -
449A PHE* 4.0 13.2 - - + -
463A LEU* 3.7 31.0 - - + -
510A ILE* 4.3 7.2 - - + -
511A PHE 3.3 17.9 - - - +
512A LEU* 3.7 23.6 - - + -
517A GLY 3.7 0.6 + - - -
518A TYR* 1.3 74.1 - - - +
520A ALA* 1.3 59.5 - - - +
521A VAL* 4.0 15.9 - - + -
529A LEU 3.6 0.7 - - - +
530A VAL* 3.3 4.2 - - - +
531A LEU* 2.6 43.9 + - + +
577A PHE* 3.6 26.7 - - + -
596A LEU* 4.3 1.6 - - - -
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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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510A ILE* 3.5 0.5 - - - -
511A PHE* 2.8 39.6 + - + +
519A LEU* 1.3 73.3 - - - +
521A VAL* 1.3 62.2 - - - +
528A VAL* 5.7 1.1 - - + -
529A LEU 3.4 6.3 - - - +
530A VAL* 4.8 4.0 - - + -
594A LEU* 3.4 20.8 - - + +
596A LEU* 3.7 34.7 - - + +
603A VAL* 4.6 9.0 - - + -
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Residues in contact with VAL 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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447A VAL* 4.2 18.8 - - + -
463A LEU* 5.2 1.1 - - + -
465A THR* 4.3 16.2 - - + -
507A ILE* 4.4 13.9 - - + -
509A LYS 3.3 5.6 - - - +
510A ILE* 4.2 11.0 - - + -
519A LEU* 4.0 26.9 - - + -
520A ALA* 1.3 79.7 - - - +
522A ALA* 1.3 61.5 + - - +
527A GLN 4.2 0.2 - - - +
528A VAL* 3.5 4.9 - - - +
529A LEU* 2.9 57.4 + - + +
531A LEU* 3.8 8.7 - - + -
594A LEU* 4.3 1.3 - - - -
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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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507A ILE* 3.4 7.4 - - - +
508A GLN* 2.6 32.7 + - - -
509A LYS* 2.9 24.5 + - + +
521A VAL* 1.3 76.0 - - - +
523A GLY* 1.3 53.8 + - - +
527A GLN 3.4 4.9 - - - +
528A VAL* 4.5 5.6 - - + +
591A VAL* 3.6 35.2 - - + -
594A LEU* 4.1 7.0 - - + -
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Residues in contact with GLY 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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506A GLY 3.2 11.2 - - - -
507A ILE* 4.4 3.8 - - - -
508A GLN* 3.6 9.9 - - - +
522A ALA* 1.3 72.1 - - - +
524A THR* 1.3 64.4 + - - -
525A ALA 3.5 1.8 - - - -
526A GLY 3.7 0.5 + - - -
527A GLN* 2.8 35.1 + - - +
591A VAL* 3.6 21.7 + - - +
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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