Contacts of the helix formed by residues 432 - 438 (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 THR 432 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460A THR 3.1 22.7 - - - +
461A LEU* 4.6 1.6 - - - -
462A ALA* 4.9 0.8 - - + +
392B MET* 4.3 14.0 - - - +
393B ILE 3.4 11.0 + - - +
394B ILE* 2.8 44.2 - - + +
431B GLU* 1.3 84.9 + - - +
433B PRO* 1.4 62.6 - - + +
434B ALA* 3.3 9.6 - - + +
435B ALA* 3.2 5.5 + - - +
436B ALA 2.9 23.2 + - - -
456B LEU* 3.0 10.2 - - - +
459B TYR* 4.4 3.4 - - - -
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Residues in contact with PRO 433 (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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433A PRO* 3.6 26.9 - - + -
459A TYR 3.2 21.3 - - - +
460A THR* 3.3 20.9 - - + +
484A LEU* 5.3 1.1 - - + -
432B THR* 1.4 80.3 - - + +
434B ALA* 1.3 57.6 - - - +
436B ALA* 3.7 5.6 - - + +
437B THR* 2.6 35.1 + - - +
456B LEU* 3.5 8.7 - - + -
459B TYR* 3.5 20.2 - - + -
460B THR* 3.6 17.5 - - - +
484B LEU* 4.6 6.6 - - + +
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Residues in contact with ALA 434 (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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460A THR* 2.9 29.4 + - - +
461A LEU* 3.8 9.2 - - + -
480A SER* 3.7 17.6 - - - +
394B ILE* 3.2 22.2 - - + +
432B THR* 3.3 7.6 - - + -
433B PRO* 1.3 75.2 - - - +
435B ALA* 1.3 65.2 + - - +
437B THR* 2.8 14.2 + - - -
438B ILE* 3.0 16.7 + - - +
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Residues in contact with ALA 435 (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 3.4 22.0 - - - +
394B ILE 4.3 1.3 + - - -
429B MET 4.5 2.0 - - - +
430B VAL* 3.7 24.0 - - + +
432B THR* 3.2 11.7 + - - +
434B ALA* 1.3 79.2 - - - +
436B ALA* 1.3 57.4 - - - +
438B ILE* 3.2 4.3 + - - -
439B ALA* 2.8 32.1 + - - +
442B LEU* 3.6 26.7 - - + +
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Residues in contact with ALA 436 (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* 3.6 11.9 - - + +
432B THR 2.9 16.7 + - - +
433B PRO* 3.7 7.9 - - + +
435B ALA* 1.3 75.4 - - - +
437B THR* 1.3 62.7 + - - +
439B ALA* 3.1 18.2 - - - +
456B LEU* 4.2 6.1 - - + -
484B LEU* 3.9 28.3 - - + +
487B GLN* 3.6 13.2 - - - +
488B VAL* 3.8 18.5 - - + +
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Residues in contact with THR 437 (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 4.4 0.4 - - - +
480A SER* 3.4 34.1 - - - +
483A ASN* 3.9 22.1 + - + +
484A LEU* 3.8 26.4 - - + +
433B PRO* 2.6 17.7 + - - +
434B ALA 2.8 10.1 + - - -
436B ALA* 1.3 77.0 - - - +
438B ILE* 1.3 56.3 + - + +
439B ALA 3.3 1.2 + - - -
440B ARG 5.0 1.0 + - - -
441B HIS* 5.6 0.3 - - - -
484B LEU* 4.7 5.0 - - - +
487B GLN* 4.2 13.2 + - - +
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Residues in contact with ILE 438 (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* 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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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