Contacts of the helix formed by residues 490 - 497 (chain B) 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 HIS 490 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313B MET* 4.0 26.9 - - + -
314B TRP* 4.4 21.8 - + + +
486B PHE* 2.8 41.4 + + + +
487B GLN* 3.4 8.6 - - - +
489B LEU* 1.3 103.7 + - + +
491B PRO* 1.4 66.9 - - - +
492B ILE 3.3 3.1 + - - -
493B VAL* 3.8 26.6 + - + +
494B VAL* 4.3 8.0 + - - +
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Residues in contact with PRO 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B GLN* 3.1 24.6 + - + +
488B HIS* 4.2 7.9 - - - +
489B LEU 3.9 5.2 - - - +
490B HIS* 1.4 87.1 - - - +
492B ILE* 1.3 76.6 + - + +
494B VAL* 4.4 4.2 + - - +
495B GLN* 3.3 23.0 + - - +
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Residues in contact with ILE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490B HIS 3.3 0.6 - - - -
491B PRO* 1.3 95.3 - - + +
493B VAL* 1.3 69.0 + - + +
494B VAL 3.2 2.2 - - - -
495B GLN* 3.2 18.0 + - + +
496B ALA* 3.0 22.8 + - + +
500P LEU* 6.2 0.2 - - + -
503P LEU* 3.9 48.9 - - + +
504P LEU* 3.8 28.5 - - + -
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Residues in contact with VAL 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A GLN* 4.6 5.8 - - - +
314B TRP* 3.8 36.1 - - + +
318B GLU* 3.5 24.5 - - - +
486B PHE* 4.4 2.9 - - + -
490B HIS* 4.0 23.1 - - + +
491B PRO 3.7 0.6 - - - -
492B ILE* 1.3 77.6 - - + +
494B VAL* 1.3 54.0 + - - +
496B ALA* 4.8 2.9 - - - -
497B ALA* 2.7 35.1 + - + +
498B PHE* 3.5 20.2 + - + -
504P LEU* 5.8 4.7 - - + -
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Residues in contact with VAL 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A PRO* 5.1 0.5 - - - +
483B LEU* 4.5 8.1 - - + -
486B PHE* 3.9 30.3 - - + -
487B GLN* 4.4 22.9 - - + +
490B HIS 4.3 3.0 + - - +
491B PRO 4.7 2.9 - - - +
492B ILE 3.2 0.6 - - - -
493B VAL* 1.3 73.2 - - - +
495B GLN* 1.3 65.7 + - + +
496B ALA 3.4 0.2 + - - -
498B PHE* 3.3 49.6 + - + +
502B TYR* 5.7 0.7 - - + -
503B LYS* 4.4 25.0 - - + +
507B SER* 4.3 17.7 - - - +
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Residues in contact with GLN 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A PRO* 3.3 25.3 - - - +
491B PRO* 3.3 21.2 + - - +
492B ILE* 3.2 18.7 + - - +
494B VAL* 1.3 77.5 - - + +
496B ALA* 1.3 58.4 + - + +
503B LYS* 3.9 26.4 - - - +
500P LEU* 3.7 15.1 - - + +
503P LEU* 3.5 26.2 - - + +
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Residues in contact with ALA 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A GLN* 5.8 1.8 - - - +
499A PRO 4.0 0.3 - - - -
500A PRO* 3.4 6.7 - - - +
501A LEU* 2.9 35.4 + - + +
492B ILE* 3.0 17.5 + - + +
493B VAL* 4.1 2.2 - - - +
495B GLN* 1.3 78.5 - - - +
497B ALA* 1.3 61.3 + - + +
500P LEU* 4.0 20.0 - - + +
504P LEU* 4.2 32.1 - - + -
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Residues in contact with ALA 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A HIS* 4.9 4.0 + - - -
325A THR* 4.8 4.0 - - + -
329A GLN* 3.5 18.4 - - - +
499A PRO* 3.6 22.9 - - - +
500A PRO* 4.2 1.1 - - - -
501A LEU* 6.4 0.2 - - + -
318B GLU* 3.3 41.7 - - - +
493B VAL 2.7 17.4 + - - +
496B ALA* 1.3 75.6 - - + +
498B PHE* 1.3 65.9 + - - +
499B PRO* 3.8 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