Contacts of the strand formed by residues 385 - 395 (chain B) in PDB entry 4NPJ
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 GLY 385 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383B PRO* 3.3 7.4 - - - +
384B LYS* 1.3 81.5 - - - +
386B VAL* 1.3 66.0 + - - +
446B VAL 3.0 24.5 + - - +
505B TRP* 3.9 14.2 - - - -
506B LEU 3.1 14.8 - - - -
508B LEU* 3.7 10.3 - - - -
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Residues in contact with VAL 386 (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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385B GLY* 1.3 78.8 - - - +
387B LEU* 1.3 72.0 + - - +
388B ARG 4.6 0.2 - - - +
443B GLU* 4.2 15.0 - - + -
444B ALA 3.4 17.0 - - - +
445B LEU* 4.0 11.2 - - + -
504B GLU 3.5 1.2 - - - +
505B TRP* 3.8 3.0 - - - -
506B LEU* 2.8 48.0 + - + +
537B LEU* 3.9 20.0 - - + -
591B PHE* 4.3 5.6 - - + -
655B LEU* 3.5 35.4 - - + -
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Residues in contact with LEU 387 (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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386B VAL* 1.3 72.5 - - - +
388B ARG* 1.3 59.9 + - - +
389B ILE* 3.8 29.9 + - + +
420B VAL* 4.4 8.3 - - + -
443B GLU* 3.5 1.2 - - - -
444B ALA* 2.8 39.5 + - + +
446B VAL* 4.0 18.1 - - + +
454B LEU* 4.4 12.3 - - + -
476B LEU* 3.6 26.5 - - + -
479B VAL* 3.7 29.2 - - + -
503B LEU* 4.5 9.6 - - + -
504B GLU 3.6 15.0 - - - +
505B TRP* 4.3 9.9 - - + -
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Residues in contact with ARG 388 (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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386B VAL 3.7 1.8 + - - -
387B LEU* 1.3 71.9 - - - +
389B ILE* 1.3 62.5 + - - +
390B HIS* 3.9 11.7 - - - +
441B VAL* 3.7 22.7 - - + -
442B TYR 3.4 5.8 - - - +
443B GLU* 2.9 24.6 + - + +
502B ARG 3.7 1.7 - - - +
503B LEU* 3.6 4.9 - - - -
504B GLU* 2.9 66.9 + - + +
506B LEU* 3.6 32.0 - - + +
521B ASP* 6.3 0.8 - - - +
522B ILE* 4.1 15.1 - - - +
533B LEU* 4.0 14.5 - - - +
534B SER 2.8 31.5 + - - +
655B LEU* 5.4 0.2 - - - +
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Residues in contact with ILE 389 (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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387B LEU* 3.8 26.0 - - + +
388B ARG* 1.3 74.9 - - - +
390B HIS* 1.3 69.8 + - - +
391B PHE* 3.5 5.1 + - + +
418B ILE* 3.9 21.5 - - + -
420B VAL* 3.9 16.4 - - + -
425B PHE* 4.9 1.6 - - + -
441B VAL* 3.1 4.1 - - - -
442B TYR* 2.7 55.0 + - + +
444B ALA* 4.7 4.5 - - + -
454B LEU* 3.8 27.8 - - + -
456B ILE* 5.2 1.3 - - + -
501B LEU* 4.9 8.3 - - + -
502B ARG 4.0 1.6 - - - -
503B LEU* 4.0 16.2 - - + -
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Residues in contact with HIS 390 (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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388B ARG* 3.9 13.0 - - - -
389B ILE* 1.3 75.6 - - - +
391B PHE* 1.3 59.8 + - - +
392B ILE* 3.3 16.3 + - + +
440B GLU 3.5 5.4 - - - +
441B VAL* 3.8 17.2 - - + +
501B LEU* 3.4 9.5 - - - +
502B ARG* 2.8 79.6 + - + +
504B GLU* 3.2 25.0 + - - -
525B ASP* 3.2 27.1 - - - -
527B ASP* 2.9 20.5 + - - +
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Residues in contact with PHE 391 (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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389B ILE* 3.5 3.8 + - + -
390B HIS* 1.3 68.0 - - - +
392B ILE* 1.3 60.0 + - - +
393B GLU 4.0 0.2 - - - -
416B GLY* 3.9 7.0 - - - -
418B ILE* 4.0 17.9 - - + -
427B SER* 3.6 25.8 - - - -
438B TRP* 3.3 41.8 - + + +
439B ASN 3.3 4.9 + - - -
440B GLU 2.7 29.9 + - - +
442B TYR* 3.6 26.0 - + + -
456B ILE* 4.2 7.0 - - + -
458B LEU* 3.5 27.6 - - + -
499B LEU* 3.8 25.1 - - + -
501B LEU* 3.8 16.2 - - + -
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Residues in contact with ILE 392 (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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390B HIS* 3.3 19.8 + - + +
391B PHE* 1.3 73.6 - - - +
393B GLU* 1.3 71.9 + - + +
437B LYS* 3.5 1.0 - - - -
438B TRP* 2.8 27.3 + - - -
439B ASN* 2.9 30.7 + - - +
486B ASP* 4.2 1.3 - - - +
500B HIS* 3.4 54.2 + - + +
502B ARG* 3.8 26.0 - - + +
527B ASP* 5.4 5.6 - - - +
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Residues in contact with GLU 393 (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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391B PHE 4.0 0.2 - - - -
392B ILE* 1.3 90.1 - - + +
394B ALA* 1.3 60.0 + - - +
436B PRO 3.3 14.6 - - - +
437B LYS* 3.7 32.1 + - + +
438B TRP* 3.8 9.5 - - - -
488B TRP* 3.7 19.9 - - + -
499B LEU* 3.5 4.7 - - - +
500B HIS* 2.8 65.8 + - + +
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Residues in contact with ALA 394 (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 GLU* 1.3 79.5 - - - +
395B GLN* 1.3 64.4 + - - +
397B LEU* 4.0 16.4 - - + -
435B SER* 3.2 21.7 - - - -
436B PRO* 3.0 20.3 + - + +
437B LYS* 5.4 0.5 + - - -
438B TRP* 3.7 23.7 - - + -
458B LEU* 4.7 1.3 - - + -
488B TRP* 4.2 3.7 - - - -
498B LYS 3.2 14.6 - - - +
499B LEU* 4.3 5.4 - - + -
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Residues in contact with GLN 395 (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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394B ALA* 1.3 78.1 - - - +
396B ASP* 1.3 78.0 + - + +
397B LEU* 3.3 3.9 + - - +
434B LEU 3.7 0.7 - - - -
435B SER* 3.9 13.0 - - - +
488B TRP* 3.6 34.0 - - + -
497B GLY* 3.5 0.3 - - - -
498B LYS* 2.9 50.2 + - + +
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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