Contacts of the helix formed by residues 520 - 525 (chain A) in PDB entry 5IYB
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 MET 520 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ASP* 4.2 8.3 - - - +
455A ILE* 3.5 36.8 - - + -
471A GLY* 3.2 26.7 - - - +
472A HIS* 4.1 3.6 - - - -
473A ARG* 4.7 13.5 - - + -
515A ILE 3.2 4.8 + - - +
516A GLN* 3.6 39.5 - - + +
518A LEU 3.3 2.6 + - - -
519A ALA* 1.3 79.2 - - - +
521A VAL* 1.3 65.5 + - - +
522A PRO* 3.6 17.7 - - + -
523A ARG* 3.2 21.4 + - + +
524A MET* 3.2 7.6 + - - +
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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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375A ILE* 4.2 12.3 - - + -
376A ASP* 3.6 15.5 - - + -
470A MET* 4.3 19.1 - - + -
471A GLY 3.1 18.1 + - - +
472A HIS* 3.6 30.1 - - + +
488A VAL* 4.6 5.2 - - + -
519A ALA 3.6 0.6 + - - -
520A MET* 1.3 70.8 - - - +
522A PRO* 1.3 61.0 - - + +
524A MET* 2.9 27.1 + - - +
525A ILE 3.6 1.4 + - - -
535A MET* 3.8 16.3 - - + +
666A ARG* 2.5 28.8 + - - +
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Residues in contact with PRO 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASP* 3.3 27.6 - - + +
520A MET* 3.5 13.9 - - + -
521A VAL* 1.3 89.8 - - + +
523A ARG* 1.3 54.5 + - + +
525A ILE* 3.2 19.6 - - + +
657A TYR* 3.6 2.4 - - - -
662A HIS* 3.2 42.4 - - + +
663A ASP* 5.3 0.2 - - - -
666A ARG* 2.9 44.4 - - + +
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Residues in contact with ARG 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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467A MET* 4.7 2.3 - - - +
516A GLN 4.8 2.0 - - - +
517A GLU* 3.2 26.1 + - - +
518A LEU 3.5 15.0 - - - +
520A MET* 3.4 20.6 - - + +
521A VAL 3.1 0.4 - - - -
522A PRO* 1.3 75.0 - - - +
524A MET* 1.3 69.8 + - + +
525A ILE 3.2 2.2 + - - -
526A VAL 5.0 2.3 + - - +
657A TYR* 3.6 16.2 + - - -
662A HIS* 3.5 40.3 + - - -
899A GLU* 5.2 8.1 + - - +
59F LYS* 5.3 12.4 - - - +
62F ARG* 3.4 26.2 - - - +
127F ASP* 3.7 25.1 + - - -
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Residues in contact with MET 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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466A LYS* 4.4 5.4 - - - +
467A MET* 2.9 49.9 - - + +
470A MET* 3.5 31.9 - - + +
518A LEU 3.4 25.1 - - - +
519A ALA 3.6 7.2 - - - +
520A MET 3.4 11.0 - - - +
521A VAL 2.9 12.2 + - - +
523A ARG* 1.3 85.2 - - + +
525A ILE* 1.3 62.6 + - - +
526A VAL 3.6 1.1 - - - -
534A VAL* 3.5 5.2 - - - +
535A MET* 4.3 2.7 - - + -
899A GLU* 5.7 2.7 - - - +
1097B HIS* 3.3 34.5 - - + +
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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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522A PRO* 3.2 18.8 - - + +
523A ARG 3.2 4.4 + - - -
524A MET* 1.3 77.7 - - - +
526A VAL* 1.3 64.8 + - + +
533A PRO* 3.5 7.1 - - + +
534A VAL* 2.9 28.2 + - - +
535A MET* 3.9 11.7 - - + -
653A VAL* 5.5 1.8 - - + +
657A TYR* 3.5 31.1 + - + -
662A HIS 4.3 3.4 - - - +
665A THR* 3.8 23.3 - - + -
666A ARG* 3.2 35.7 - - - +
669A TYR* 4.3 21.8 - - + +
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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