Contacts of the helix formed by residues 490 - 498 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313C MET* 4.2 26.5 - - + -
314C TRP* 4.3 23.4 - + + -
486C PHE* 2.8 36.4 + + + +
487C GLN 3.6 3.1 - - - -
489C LEU* 1.3 99.2 + - + +
491C PRO* 1.3 65.5 - - - +
492C ILE 3.3 3.9 + - - -
493C VAL* 3.5 24.9 + - + -
494C VAL* 3.7 17.2 + - - +
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Residues in contact with PRO 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C GLN* 3.2 25.4 + - + +
488C HIS 3.7 7.0 - - - +
489C LEU 3.6 7.6 - - - +
490C HIS* 1.3 89.1 - - - +
492C ILE* 1.3 78.5 + - + +
494C VAL* 3.9 4.9 + - - +
495C GLN* 3.7 23.3 + - - +
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Residues in contact with ILE 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490C HIS 3.3 1.0 - - - -
491C PRO* 1.3 91.2 - - + +
493C VAL* 1.3 61.9 + - + +
494C VAL 3.2 0.4 - - - -
495C GLN* 3.1 14.2 + - + +
496C ALA* 2.9 33.2 + - + +
500S LEU 4.8 0.4 - - - +
503S LEU* 3.8 50.9 - - + +
504S LEU* 4.2 28.3 - - + +
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Residues in contact with VAL 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C TRP* 3.8 30.5 - - + +
318C GLU* 3.1 26.9 - - - +
486C PHE* 4.0 2.5 - - + -
490C HIS* 3.5 29.6 + - + +
491C PRO 3.5 0.2 - - - -
492C ILE* 1.3 78.4 - - + +
494C VAL* 1.3 56.4 + - - +
496C ALA* 5.0 2.0 - - - -
497C ALA 2.9 27.6 + - - +
498C PHE* 3.5 22.1 + - + -
329D GLN* 4.7 7.9 - - - +
504S LEU* 5.7 5.6 - - + +
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Residues in contact with VAL 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483C LEU* 4.9 2.9 - - + -
486C PHE* 3.7 22.7 - - + -
487C GLN* 3.8 39.5 - - + +
490C HIS 3.7 15.2 + - - +
491C PRO 4.0 6.5 - - - +
492C ILE 3.2 0.4 - - - -
493C VAL* 1.3 78.3 - - - +
495C GLN* 1.3 63.4 + - + +
498C PHE* 3.3 43.3 + - + +
502C TYR* 6.2 0.4 - - + -
503C LYS* 4.2 22.1 - - + +
507C SER* 4.2 10.8 - - - +
500D PRO* 5.2 0.2 - - - +
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Residues in contact with GLN 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491C PRO* 3.7 14.6 + - - +
492C ILE* 3.1 18.8 + - + +
494C VAL* 1.3 79.7 - - + +
496C ALA* 1.3 57.8 + - - +
503C LYS* 5.0 17.7 - - - +
500D PRO* 3.3 24.1 - - - +
500S LEU* 3.6 17.1 - - + +
503S LEU* 3.9 27.8 - - - +
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Residues in contact with ALA 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492C ILE* 2.9 21.0 + - + +
493C VAL* 4.4 1.6 - - - +
495C GLN* 1.3 78.2 - - - +
497C ALA* 1.3 61.5 + - + +
329D GLN* 5.9 2.0 - - - +
499D PRO 4.1 0.2 - - - -
500D PRO* 3.3 5.4 - - - +
501D LEU* 2.7 41.1 + - + +
500S LEU* 3.8 26.5 - - + -
504S LEU* 4.5 16.8 - - + -
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Residues in contact with ALA 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C GLU* 3.2 42.2 - - - +
493C VAL 2.9 8.9 + - - +
496C ALA* 1.3 79.0 - - + +
498C PHE* 1.3 67.6 + - - +
499C PRO* 3.7 3.8 - - - +
322D HIS* 4.8 5.8 + - - +
325D THR* 4.6 6.3 - - + -
329D GLN* 3.7 16.6 - - - +
499D PRO* 3.5 23.2 - - - +
500D PRO* 4.1 1.8 - - - -
501D LEU* 5.7 0.2 - - + -
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Residues in contact with PHE 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317C TRP* 3.8 23.1 - + + -
318C GLU* 3.6 27.6 - - + -
321C ALA* 3.8 10.5 - - + -
483C LEU* 4.2 12.6 - - + -
486C PHE* 3.5 22.7 - + - -
493C VAL* 3.5 30.0 + - + -
494C VAL* 3.3 31.3 + - + +
497C ALA* 1.3 76.8 - - - +
499C PRO* 1.4 73.8 - - + +
500C PRO* 3.3 1.4 - - - +
502C TYR* 3.6 35.7 - + + -
503C LYS* 5.5 3.2 - - + +
500D PRO* 3.3 21.2 - - - +
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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