Contacts of the helix formed by residues 521 - 529 (chain A) in PDB entry 4I5L
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 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A ILE* 3.7 33.9 - - + -
486A VAL* 5.1 3.6 - - + -
487A LEU* 4.7 3.8 - - + -
505A ILE* 3.7 41.1 - - + +
508A LEU* 3.4 46.7 - - + -
509A SER* 4.6 9.0 - - - -
512A CYS* 5.2 1.3 - - - -
516A ILE* 3.5 7.4 + - - +
517A THR* 3.1 21.9 + - + +
520A HIS* 1.3 84.0 - - - +
522A LEU* 1.3 65.9 + - - +
523A PRO* 3.4 2.9 - - - +
524A THR* 3.3 15.8 + - - -
525A VAL* 3.3 16.3 + - - +
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Residues in contact with LEU 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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517A THR* 2.9 16.6 + - - +
518A THR* 3.6 10.5 - - + +
521A MET* 1.3 73.6 - - - +
523A PRO* 1.3 70.4 - - + +
525A VAL* 3.1 7.8 + - + -
526A LEU* 3.0 39.0 + - + +
544A LEU* 3.7 29.2 - - + -
547A ILE* 4.3 8.5 - - + -
551A LEU* 4.0 26.0 - - + -
555A THR* 3.5 31.9 - - + -
559A GLU* 4.0 11.4 - - - +
560A VAL* 4.2 4.9 - - + -
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Residues in contact with PRO 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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518A THR 3.5 15.5 - - - +
519A LYS* 3.4 17.7 - - - +
520A HIS 4.1 2.0 - - - -
521A MET* 3.4 12.3 - - - +
522A LEU* 1.3 88.5 - - + +
524A THR* 1.3 55.8 + - - +
526A LEU* 3.5 10.5 + - + +
527A ARG* 3.0 29.7 + - - +
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Residues in contact with THR 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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487A LEU* 3.6 39.6 - - + +
490A SER* 3.9 28.3 - - - +
501A THR* 4.4 4.7 - - + -
505A ILE* 4.7 1.6 - - + -
520A HIS 4.8 1.2 + - - -
521A MET 3.3 10.1 + - - -
522A LEU 3.2 0.8 - - - -
523A PRO* 1.3 76.3 - - - +
525A VAL* 1.3 65.6 + - - +
527A ARG* 3.2 20.4 + - - +
528A MET* 2.9 36.2 + - - +
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Residues in contact with VAL 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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502A LEU* 4.1 21.8 - - + -
505A ILE* 3.8 29.8 - - + -
521A MET 3.3 14.3 + - - +
522A LEU* 3.1 12.7 + - - +
524A THR* 1.3 76.3 - - - +
526A LEU* 1.3 62.8 + - - +
528A MET* 3.0 13.5 + - - +
529A ALA 3.5 7.3 + - - -
540A VAL* 3.6 20.5 - - + +
543A SER* 4.3 6.5 - - - -
544A LEU* 3.5 33.9 - - + -
547A ILE* 4.6 6.3 - - + -
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Residues in contact with LEU 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 LEU* 3.0 44.4 + - + +
523A PRO* 3.8 8.1 - - + +
525A VAL* 1.3 74.8 - - - +
527A ARG* 1.3 62.5 + - - +
529A ALA* 3.2 19.2 + - - +
530A GLY 4.6 0.2 + - - -
540A VAL* 5.1 0.4 - - - -
544A LEU* 4.0 21.8 - - + -
559A GLU* 3.9 39.3 - - + +
560A VAL* 4.5 3.8 - - - -
563A ILE* 3.9 36.1 - - + +
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Residues in contact with ARG 527 (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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490A SER* 2.9 36.0 + - - -
491A GLY* 5.9 0.2 - - - -
523A PRO 3.0 16.8 + - - +
524A THR* 3.2 21.1 + - - +
526A LEU* 1.3 75.4 - - - +
528A MET* 1.3 66.4 + - - +
529A ALA 3.1 1.3 + - - -
530A GLY* 3.3 13.9 + - - -
531A ASP 4.6 0.5 + - - -
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Residues in contact with MET 528 (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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490A SER* 3.8 31.2 - - - +
498A ARG* 3.4 37.0 - - + +
501A THR* 4.4 3.8 - - - -
502A LEU* 3.9 22.4 - - + -
524A THR* 2.9 26.7 + - + +
525A VAL 3.0 8.9 + - - +
527A ARG* 1.3 80.7 - - - +
529A ALA* 1.3 58.7 + - - +
530A GLY 3.1 2.5 - - - -
531A ASP* 3.0 31.3 + - + +
536A VAL* 3.7 24.0 - - + +
537A ARG* 4.4 1.4 - - - +
540A VAL* 3.5 17.1 - - + +
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Residues in contact with ALA 529 (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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525A VAL 3.5 3.8 + - - -
526A LEU 3.2 15.8 + - - +
527A ARG 3.1 1.2 - - - -
528A MET* 1.3 77.8 - - - +
530A GLY* 1.3 55.4 + - - +
531A ASP 3.3 0.7 - - - -
537A ARG* 3.0 26.5 - - - +
540A VAL* 3.6 18.1 - - + +
563A ILE* 3.6 27.8 - - + -
566A LYS* 6.3 2.9 - - + -
567A LEU* 3.7 17.0 - - + +
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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