Contacts of the strand formed by residues 398 - 403 (chain B) in PDB entry 3NVN
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 GLN 398 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373B HIS* 5.2 5.0 + - - -
392B LEU 3.4 4.5 - - - +
393B GLY* 3.5 2.9 - - - -
394B THR* 2.9 36.0 + - - +
396B ASP* 3.7 20.9 - - - +
397B GLY* 1.3 78.6 - - - +
399B LEU* 1.3 60.4 + - - +
400B LEU* 3.8 18.6 - - + +
415B VAL* 3.4 28.0 - - + +
417B TYR 3.5 3.6 - - - +
418B GLU* 3.1 34.6 + - + +
425B VAL* 4.0 3.7 - - - +
441B LEU* 5.8 0.2 - - - -
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Residues in contact with LEU 399 (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* 4.2 17.3 - - + -
392B LEU 3.2 23.1 - - - +
393B GLY* 4.6 0.4 - - - +
397B GLY 4.1 0.4 + - - -
398B GLN* 1.3 72.7 - - - +
400B LEU* 1.3 67.2 + - - +
415B VAL* 3.9 0.7 - - - -
416B ILE* 2.9 36.5 + - + +
417B TYR* 2.9 22.1 + - + +
429B LEU* 4.2 16.8 - - + -
439B ILE* 4.0 27.8 - - + -
441B LEU* 4.4 24.7 - - + -
450B ILE* 4.2 20.4 - - + -
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 5.6 1.3 - - + -
373B HIS* 4.0 19.5 - - + +
376B LEU* 4.1 12.6 - - + -
391B PHE* 3.3 7.1 - - - +
392B LEU* 2.7 40.3 + - + +
394B THR* 3.5 30.5 - - + -
398B GLN* 4.2 20.0 - - + +
399B LEU* 1.3 77.2 - - - +
401B LYS* 1.3 62.7 + - - +
413B PRO* 4.2 22.4 - - + +
414B GLU 3.4 5.6 - - - +
415B VAL* 3.9 28.9 - - + +
416B ILE* 4.8 0.4 - - - -
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Residues in contact with LYS 401 (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 VAL* 3.6 25.8 - - + -
390B LEU 3.3 6.3 - - - +
391B PHE* 3.9 14.4 - - + -
400B LEU* 1.3 78.2 - - - +
402B VAL* 1.3 64.2 + - - +
403B ILE* 4.3 12.5 + - + +
411B ASN* 5.0 1.7 + - - -
412B CYS 4.5 0.9 - - - +
413B PRO* 3.4 2.8 - - - +
414B GLU* 2.9 32.0 + - + +
416B ILE* 3.4 24.5 - - + -
452B VAL 3.0 25.6 + - - +
453B ALA* 3.5 3.6 - - + +
469B ASP* 2.9 29.1 + - - +
471B HIS* 2.9 29.9 - - - -
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Residues in contact with VAL 402 (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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328B LEU* 5.6 1.6 - - + -
371B LEU* 4.1 14.8 - - + -
388B THR 3.6 1.4 - - - +
389B VAL* 3.6 2.1 - - - -
390B LEU* 2.8 52.0 + - + +
392B LEU* 3.8 16.8 - - + -
401B LYS* 1.3 79.0 - - - +
403B ILE* 1.3 64.5 + - - +
404B LEU* 4.0 19.7 + - + -
410B SER* 4.3 6.1 - - - -
411B ASN* 3.2 28.9 - - - +
413B PRO* 3.8 23.8 - - + -
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Residues in contact with ILE 403 (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 ARG* 4.1 27.0 + - + +
388B THR 3.5 4.5 - - - +
389B VAL* 4.5 10.5 - - + -
401B LYS* 4.4 13.4 + - + +
402B VAL* 1.3 78.2 - - - +
404B LEU* 1.3 71.6 + - - +
405B GLY 3.8 1.2 + - - -
411B ASN* 2.6 42.2 + - - +
414B GLU* 6.1 0.4 - - - +
467B ALA 5.0 2.5 - - - +
468B THR* 3.3 29.2 - - - +
469B ASP* 3.6 30.5 - - + +
470B PRO* 3.7 11.0 - - + -
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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