Contacts of the strand formed by residues 446 - 451 (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 GLU 446 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 4.4 4.0 - - + -
40B TRP 3.3 4.3 - - - +
41B ARG* 3.1 47.0 + - + -
46B ILE* 3.7 2.3 - - - +
419B ILE* 4.9 0.2 - - - +
421B GLU* 4.2 14.5 - - - +
423B THR* 4.4 9.7 + - - -
441B LEU 3.8 0.7 - - - +
442B THR* 3.4 2.8 - - - -
443B ALA* 2.9 37.4 + - + +
444B GLY 3.5 0.4 - - - -
445B LYS* 1.3 84.9 + - + +
447B VAL* 1.3 64.0 + - - +
448B ARG* 3.1 37.5 + - - +
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.4 1.4 - - - +
40B TRP* 2.9 44.6 + - + +
46B ILE* 3.1 28.5 - - + -
49B ILE* 5.1 9.9 - - + -
57B VAL* 5.7 0.2 - - + -
59B VAL* 4.1 20.4 - - + -
68B LEU* 5.5 0.2 - - + -
72B LEU* 3.3 26.5 - - + +
440B TYR* 4.4 12.3 - - + -
441B LEU 3.4 4.3 - - - +
442B THR* 3.9 17.9 - - - +
446B GLU* 1.3 73.8 - - - +
448B ARG* 1.3 66.1 + - - +
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Residues in contact with ARG 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLU* 5.3 4.5 - - + -
38B PRO 3.4 9.6 - - - +
39B VAL* 3.2 28.8 - - + +
41B ARG* 4.5 5.7 - - - +
72B LEU* 3.5 5.8 - - - -
417B TYR* 3.4 40.8 + - - -
419B ILE* 3.4 31.3 - - - +
420B LYS* 5.2 0.8 - - - +
421B GLU* 3.7 6.5 + - - -
440B TYR* 3.4 6.9 - - - +
441B LEU* 2.7 40.8 + - + +
443B ALA* 6.3 0.4 - - - +
446B GLU* 3.1 37.9 + - + +
447B VAL* 1.3 79.0 - - - +
449B ARG* 1.3 58.6 + - - +
450B ILE* 3.2 16.2 - - + +
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Residues in contact with ARG 449 (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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37B GLU* 3.3 22.7 - - - +
38B PRO* 3.2 37.9 + - + +
70B TYR* 3.1 42.0 + - - +
71B SER* 4.0 12.7 + - - +
72B LEU* 3.4 8.9 - - + +
432B ASP* 2.7 28.7 + - - -
435B LYS* 3.7 26.7 - - - +
438B TYR* 3.5 42.6 + - + -
439B ILE 4.0 2.5 - - - +
440B TYR* 3.6 12.0 + - + -
448B ARG* 1.3 72.3 - - - +
450B ILE* 1.3 60.6 + - - +
451B ARG 4.2 0.5 + - - -
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Residues in contact with ILE 450 (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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37B GLU* 5.0 7.2 - - + +
399B LEU* 4.2 9.0 - - + -
416B ILE* 3.9 18.2 - - + -
417B TYR* 4.1 33.7 - - + -
438B TYR* 3.4 5.1 - - - -
439B ILE* 2.8 45.2 + - + +
441B LEU* 3.3 24.5 - - + +
448B ARG* 3.2 42.4 - - + +
449B ARG* 1.3 74.1 - - - +
451B ARG* 1.3 76.0 + - - +
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Residues in contact with ARG 451 (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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37B GLU* 5.8 1.4 + - - +
416B ILE* 3.6 9.2 - - - +
437B ILE* 3.3 14.0 - - + +
438B TYR* 3.4 38.4 + - + -
449B ARG 4.2 0.2 + - - -
450B ILE* 1.3 87.7 - - - +
452B VAL* 1.3 63.1 + - - +
453B ALA* 3.1 17.2 + - - +
454B ASN* 5.3 2.9 - - - +
483B PHE* 4.5 16.6 - - + -
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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