Contacts of the helix formed by residues 438 - 444 (chain B) in PDB entry 2N5T
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 ILE 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A PRO* 3.9 18.8 - - + +
480A SER* 3.6 33.2 - - - +
483A ASN* 5.4 0.9 - - - +
556A PRO 5.4 0.9 - - - +
394B ILE 3.8 8.7 - - - +
395B SER* 3.7 31.4 - - - -
396B VAL* 3.7 15.0 - - + +
434B ALA 3.0 11.6 + - - +
435B ALA* 3.4 4.7 - - - +
437B THR* 1.3 78.8 - - + +
439B ALA* 1.3 66.7 + - - +
440B ARG 2.9 4.4 + - - +
441B HIS* 3.0 22.6 + - + +
442B LEU* 2.9 35.3 + - + +
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Residues in contact with ALA 439 (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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430B VAL* 5.4 0.2 - - + -
435B ALA 2.8 11.7 + - - +
436B ALA 3.1 19.1 + - - +
437B THR 3.3 1.0 - - - -
438B ILE* 1.3 77.4 - - - +
440B ARG* 1.3 62.9 + - - +
442B LEU* 4.4 5.8 - - - +
443B ALA* 2.9 26.9 + - - +
449B PHE* 3.5 9.5 - - + -
487B GLN* 4.4 3.1 - - + +
488B VAL* 4.0 19.3 - - + -
491B ALA* 3.5 20.2 - - + -
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Residues in contact with ARG 440 (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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437B THR 5.0 0.8 + - - -
438B ILE* 2.9 1.6 + - - +
439B ALA* 1.3 78.4 - - + +
441B HIS* 1.3 72.2 + - + +
443B ALA* 3.1 14.5 + - - +
444B LYS* 3.7 9.7 + - - +
487B GLN 5.3 1.4 + - - +
490B ASP* 5.0 11.5 - - - +
491B ALA* 4.0 28.7 - - + +
494B ALA* 4.3 20.2 - - - +
495B GLU* 4.8 7.8 - - - +
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Residues in contact with HIS 441 (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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479A PRO* 4.9 1.5 - - + +
483A ASN* 5.4 2.2 + - - -
553A LEU 4.6 5.9 + - - -
554A ALA* 3.1 28.8 + - - -
555A GLN 3.6 10.4 + - - -
556A PRO* 3.4 29.1 - - + +
396B VAL* 3.6 20.5 - - + +
437B THR 5.6 0.2 - - - -
438B ILE* 3.0 29.8 + - + +
440B ARG* 1.3 82.9 - - + +
442B LEU* 1.3 61.0 + - - +
444B LYS* 3.6 20.7 + - - +
445B GLU* 3.6 18.4 - - - +
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Residues in contact with LEU 442 (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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393B ILE* 4.1 9.2 - - + -
395B SER 3.7 17.5 - - - +
396B VAL* 4.0 13.5 - - + -
399B VAL* 3.6 31.0 - - + -
428B VAL* 4.8 5.8 - - + -
430B VAL* 5.3 0.4 - - + -
435B ALA* 3.6 45.5 - - + +
438B ILE* 2.9 23.7 + - + +
439B ALA* 3.8 4.7 - - - +
441B HIS* 1.3 73.4 - - - +
443B ALA* 1.3 54.9 + - - +
445B GLU* 2.7 28.8 + - + +
446B VAL* 3.2 14.3 + - + +
449B PHE* 3.9 18.8 - - + -
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Residues in contact with ALA 443 (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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439B ALA 2.9 17.3 + - - +
440B ARG* 3.1 6.5 + - - +
442B LEU* 1.3 76.6 - - - +
444B LYS* 1.3 58.7 + - - +
446B VAL* 3.2 18.3 - - - +
449B PHE* 3.4 25.1 - - + -
491B ALA 3.9 13.5 - - - +
492B SER* 4.4 1.3 - - - +
495B GLU* 3.5 29.9 - - + +
497B LYS* 4.1 8.0 - - + +
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Residues in contact with LYS 444 (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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440B ARG 3.7 6.4 + - - +
441B HIS* 3.6 20.4 + - - +
442B LEU 3.2 1.0 + - - -
443B ALA* 1.3 76.9 - - - +
445B GLU* 1.3 73.1 + - - +
446B VAL 3.5 1.2 - - - +
495B GLU* 3.9 29.4 - - - +
497B LYS* 5.4 4.8 + - - +
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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