Contacts of the helix formed by residues 499 - 507 (chain A) in PDB entry 5NTI
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 PRO 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A GLU* 5.2 1.6 - - + +
321A ALA* 4.3 15.7 - - + +
322A HIS* 3.9 21.5 - - + +
325A THR* 3.4 42.8 - - + +
497A ALA 3.6 4.2 - - - +
498A PHE* 1.3 85.8 - - + +
500A PRO* 1.3 72.8 - - + +
501A LEU 3.1 0.2 - - - -
502A TYR* 3.0 16.0 + - + +
503A LYS* 3.3 9.6 + - - +
496B ALA 4.3 1.3 - - - +
497B ALA 3.6 21.5 - - - +
498B PHE 4.4 1.1 - - - +
499B PRO* 6.4 0.4 - - + -
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Residues in contact with PRO 500 (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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498A PHE 3.5 5.8 - - - +
499A PRO* 1.3 82.0 - - + +
501A LEU* 1.3 56.2 + - - +
503A LYS* 3.4 13.1 + - + +
504A GLU* 3.0 23.0 + - - +
494B VAL 5.1 0.7 - - - +
495B GLN 3.3 24.5 - - - +
496B ALA 3.4 10.5 - - - +
498B PHE 3.1 23.6 - - - +
500B PRO* 4.0 16.6 - - + -
500P LEU* 3.4 19.0 - - + +
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Residues in contact with LEU 501 (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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325A THR* 4.1 17.7 - - + -
328A ILE* 4.1 24.2 - - + -
329A GLN* 4.5 11.7 - - + -
332A VAL* 5.0 3.8 - - + -
499A PRO 3.1 0.2 - - - -
500A PRO* 1.3 72.9 - - - +
502A TYR* 1.3 60.2 + - - +
504A GLU* 3.2 10.7 + - - +
505A LEU* 2.9 50.7 + - + +
496B ALA* 2.9 21.4 + - + +
497B ALA* 6.4 0.2 - - + -
500P LEU* 3.6 21.1 - - + +
501P LEU* 4.4 11.0 - - + +
504P LEU* 3.9 32.3 - - + -
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Residues in contact with TYR 502 (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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317A TRP* 3.4 21.3 - - - -
321A ALA* 4.0 21.8 - - + -
324A LEU* 3.7 15.9 - - + -
325A THR* 3.3 26.8 + - - +
328A ILE* 5.4 1.1 - - + -
479A HIS* 2.8 31.2 + + - -
483A LEU* 3.7 21.2 - - + +
494A VAL* 5.8 0.2 - - + -
498A PHE* 3.5 33.9 - + - -
499A PRO* 3.0 15.2 + - + +
501A LEU* 1.3 78.3 - - - +
503A LYS* 1.3 60.4 + - - +
505A LEU* 5.5 0.4 - - - -
506A PHE* 3.1 58.5 + + - +
507A SER 4.2 0.2 + - - -
601A C3S 4.3 2.9 - - + +
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Residues in contact with LYS 503 (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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483A LEU* 5.6 0.2 - - - -
487A GLN* 4.8 5.8 - - - +
494A VAL* 4.1 34.3 - - + +
495A GLN* 4.9 14.8 - - - +
498A PHE* 5.3 2.7 - - + +
499A PRO 3.3 8.8 + - - +
500A PRO* 3.7 14.1 + - + +
501A LEU 3.2 0.2 - - - -
502A TYR* 1.3 83.4 - - + +
504A GLU* 1.3 65.6 + - - +
507A SER* 3.1 45.6 + - - +
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Residues in contact with GLU 504 (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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354A LYS* 3.7 19.9 + - + +
500A PRO 3.0 17.9 + - - +
501A LEU* 3.2 9.0 + - + +
503A LYS* 1.3 79.7 - - - +
505A LEU* 1.3 65.0 + - + +
507A SER 4.8 3.8 + - - +
499P THR* 3.3 19.5 + - + +
500P LEU* 2.8 34.1 + - + +
501P LEU* 3.0 36.6 + - - +
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Residues in contact with LEU 505 (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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328A ILE* 3.8 38.8 - - + -
353A LEU 5.1 0.2 - - - +
354A LYS* 3.9 38.4 - - + +
357A ALA* 4.4 10.1 - - + -
480A VAL* 5.3 1.6 - - - +
501A LEU* 2.9 33.1 + - + +
504A GLU* 1.3 83.9 - - + +
506A PHE* 1.3 83.1 + - + +
507A SER 5.3 0.2 - - - -
501P LEU* 3.7 36.1 - - + -
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Residues in contact with PHE 506 (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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324A LEU* 4.4 1.3 - - + -
328A ILE* 3.6 33.0 - - + -
354A LYS 5.4 5.2 - - - -
357A ALA* 6.1 0.2 - - + -
358A MET* 3.7 31.6 - - + -
476A CYS* 5.9 0.4 - - + -
479A HIS* 3.4 29.8 - + + +
480A VAL* 3.7 37.7 - - + +
483A LEU* 3.6 21.1 - - + +
484A GLN* 5.9 0.2 - - - +
502A TYR* 3.1 48.5 + + - +
505A LEU* 1.3 101.0 - - + +
507A SER* 1.3 63.8 + - - +
508A THR* 3.8 0.5 + - - +
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Residues in contact with SER 507 (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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483A LEU* 3.7 9.5 - - - +
487A GLN* 2.9 34.1 + - - +
494A VAL* 5.7 0.2 - - - -
503A LYS* 3.1 37.5 + - - +
504A GLU 4.9 3.5 - - - +
505A LEU 5.3 0.2 - - - -
506A PHE* 1.3 79.5 - - - +
508A THR* 1.3 69.0 + - - +
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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