Contacts of the strand formed by residues 425 - 433 (chain B) in PDB entry 5N4D
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 425 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B PHE* 4.3 17.4 - - + -
402B VAL 4.6 5.0 + - - -
420B LEU 3.8 20.6 - - - +
421B SER* 3.4 8.1 - - - -
422B GLY* 3.1 32.4 + - - +
424B ASN* 1.3 85.1 + - - +
426B PRO* 1.3 68.4 - - + +
427B GLY 3.3 2.0 + - - +
428B THR* 4.0 18.8 - - - +
507B PHE* 3.6 2.7 - - - +
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Residues in contact with PRO 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 5.1 1.7 + - - +
421B SER* 4.5 0.4 - - - -
424B ASN 3.7 8.1 - - - +
425B THR* 1.3 88.5 - - + +
427B GLY* 1.3 58.3 + - - +
447B THR* 5.9 3.8 - - + -
448B THR* 3.7 29.5 + - + +
450B VAL* 3.6 34.8 - - + -
455B PRO* 3.9 19.1 - - + -
507B PHE* 3.5 20.6 - - + +
801B GOL 3.5 24.3 + - - -
18D LEU* 4.3 0.7 - - - +
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Residues in contact with GLY 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 4.7 1.7 - - - -
420B LEU 3.5 8.7 - - - -
425B THR* 3.3 4.6 + - - +
426B PRO* 1.3 84.6 - - - +
428B THR* 1.3 61.4 + - - +
429B ILE 4.2 0.2 + - - -
446B ARG 4.1 0.9 - - - +
447B THR* 3.7 1.7 - - - +
448B THR* 2.7 38.5 + - - -
18D LEU* 3.7 20.9 - - - +
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Residues in contact with THR 428 (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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418B LEU 3.6 0.9 - - - +
419B THR* 3.6 2.6 - - - -
420B LEU* 2.9 55.2 + - + +
425B THR* 4.0 14.7 - - - +
426B PRO* 6.0 0.2 - - - +
427B GLY* 1.3 76.2 + - - +
429B ILE* 1.3 66.3 + - - +
430B ALA 4.0 0.2 - - - -
444B ILE* 3.9 33.7 - - + -
446B ARG 3.5 9.2 - - - +
447B THR* 3.9 16.6 - - - +
18D LEU* 4.6 0.5 - - - +
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Residues in contact with ILE 429 (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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84B PHE* 3.9 26.5 - - + +
85B SER 3.3 33.9 - - - +
86B ALA* 3.6 15.7 - - + +
87B PRO* 5.1 0.7 - - + -
417B PHE* 4.1 16.4 - - + -
418B LEU 3.3 7.9 - - - +
419B THR* 4.4 4.5 - - + -
427B GLY 5.2 0.7 - - - +
428B THR* 1.3 77.5 - - - +
430B ALA* 1.3 55.1 + - - +
444B ILE* 3.7 2.3 - - - +
445B LEU* 2.8 49.7 + - + +
446B ARG* 2.8 29.5 + - + +
18D LEU* 4.0 13.7 - - + -
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Residues in contact with ALA 430 (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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417B PHE* 3.1 12.1 - - - +
418B LEU* 2.9 40.4 + - + +
420B LEU* 4.6 8.1 - - + -
428B THR 4.0 1.2 - - - -
429B ILE* 1.3 74.5 - - - +
431B ARG* 1.3 61.5 + - - +
442B PHE* 3.5 35.0 - - + -
443B SER 3.3 7.9 - - - +
444B ILE* 4.0 10.1 - - + +
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Residues in contact with ARG 431 (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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95B TRP* 5.9 0.4 - - - -
117B LEU* 3.7 31.8 - - - +
415B HIS* 4.7 9.3 - - + +
416B PHE 3.5 5.8 - - - +
417B PHE* 3.6 30.3 - - + -
429B ILE 4.4 0.2 + - - -
430B ALA* 1.3 75.0 - - - +
432B TYR* 1.3 70.2 - - - +
433B ASP* 3.7 31.6 + - - +
441B ARG 3.5 1.6 - - - +
442B PHE* 3.4 6.7 - - - -
443B SER* 2.7 55.2 + - - +
445B LEU* 4.4 12.5 - - + +
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Residues in contact with TYR 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LEU* 3.5 21.8 - - + +
395B THR* 5.2 2.7 - - + +
397B LEU* 3.9 30.3 - - + -
415B HIS* 3.1 8.3 - - - +
416B PHE* 2.9 69.4 + + + -
431B ARG* 1.3 75.2 - - - +
433B ASP* 1.3 59.2 + - - +
434B PHE* 3.7 33.7 - + - -
441B ARG* 3.2 54.2 + - + -
442B PHE* 4.3 9.9 - - + -
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Residues in contact with ASP 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B THR* 3.8 7.5 + - - +
415B HIS* 4.3 5.5 - - + +
431B ARG* 3.7 30.2 + - - +
432B TYR* 1.3 74.9 - - - +
434B PHE* 1.4 63.3 + - - +
435B THR* 2.7 36.6 + - - +
436B ALA* 3.3 23.0 + - + +
441B ARG* 2.8 30.3 + - - +
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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