Contacts of the strand formed by residues 439 - 447 (chain B) in PDB entry 1NSC
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 SER 439 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B HIS* 2.7 37.3 + - - -
113B ILE* 3.5 5.9 - - - -
114B ILE* 3.0 34.6 + - - +
115B ARG* 4.8 0.7 - - - -
429B VAL* 3.3 9.2 - - - +
430B HIS* 2.8 32.7 + - - -
437B TRP* 3.8 11.2 - - - -
438B HIS* 1.3 76.3 - - - +
440B ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 440 (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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99B PRO* 3.9 11.6 - - - +
100B HIS* 4.1 2.6 - - - -
114B ILE* 3.6 30.2 + - + +
115B ARG* 4.7 2.9 - - - -
117B PRO* 4.8 2.2 - - + -
427B GLU* 3.7 33.4 - - + +
428B MET 3.4 8.1 - - - +
429B VAL* 3.9 5.8 - - + -
430B HIS* 4.0 9.0 - - - -
439B SER* 1.3 81.8 + - - +
441B ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 4.2 7.2 - - + -
97B ILE 3.3 14.8 - - - +
98B SER* 3.8 22.9 - - - +
99B PRO* 4.1 2.7 - - - -
427B GLU* 3.6 4.3 - - - -
428B MET* 2.8 40.0 + - + +
430B HIS* 3.9 5.3 + - - +
440B ALA* 1.3 76.0 - - - +
442B THR* 1.3 62.0 + - - +
459B THR* 4.1 17.0 - - + -
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Residues in contact with THR 442 (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 LEU 4.1 0.7 - - - +
96B LEU* 3.6 3.9 - - - -
97B ILE* 2.9 33.5 + - - +
114B ILE* 5.1 2.8 - - - +
117B PRO* 3.4 16.7 - - + +
119B ILE* 4.4 11.2 - - + -
128B HIS* 3.1 39.0 + - + +
410B PHE* 4.1 27.6 - - + -
426B ILE 3.3 6.7 - - - +
427B GLU* 4.8 0.2 - - - +
440B ALA 5.1 1.0 + - - -
441B ALA* 1.3 74.8 - - - +
443B ALA* 1.3 66.7 + - - +
444B ILE* 4.4 4.8 - - + +
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Residues in contact with ALA 443 (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 LEU 3.7 4.5 - - - +
96B LEU* 4.4 2.7 - - + -
424B ILE 4.0 0.4 - - - +
425B GLY* 3.2 4.2 - - - -
426B ILE* 2.8 48.4 + - + +
428B MET* 3.9 14.1 - - - -
441B ALA 4.2 0.4 - - - -
442B THR* 1.3 73.4 - - - +
444B ILE* 1.3 62.1 + - - +
445B TYR* 4.7 3.1 - - + -
457B THR* 3.7 35.2 - - + +
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Residues in contact with ILE 444 (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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209A TYR* 5.2 2.7 - - + -
93B LYS* 4.1 0.5 - - - +
94B ALA* 2.9 29.0 + - + -
95B LEU* 2.8 51.3 + - + +
97B ILE* 4.7 3.6 - - + -
119B ILE* 3.7 32.3 - - + -
160B LEU* 4.1 8.3 - - + -
412B PHE* 3.8 19.7 - - + -
414B ILE* 5.7 0.4 - - + -
424B ILE 3.6 2.9 - - - -
425B GLY* 4.5 1.1 - - - -
442B THR* 4.4 11.4 - - + +
443B ALA* 1.3 78.4 - - - +
445B TYR* 1.3 70.6 + - - +
446B CYS* 3.7 25.6 - - - -
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Residues in contact with TYR 445 (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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91B PHE* 3.5 11.9 - - + -
92B GLN* 3.3 9.0 - - - +
93B LYS* 3.4 31.1 - - + +
399B MET* 3.1 55.6 + - + -
423B CYS* 3.3 2.9 - - - +
424B ILE* 2.8 34.8 + - + +
426B ILE* 4.1 12.1 - - + -
443B ALA* 4.7 3.1 - - + -
444B ILE* 1.3 80.1 - - - +
446B CYS* 1.3 59.5 + - - +
453B LEU* 4.0 20.2 - - + -
455B TRP 2.7 29.1 + - - -
456B ASP* 3.2 3.1 - - - -
457B THR* 2.9 30.0 + - - -
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Residues in contact with CYS 446 (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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209A TYR* 3.9 20.6 - - + -
91B PHE* 3.6 5.4 - - - -
92B GLN 2.9 29.4 + - - +
94B ALA* 4.3 1.5 - - - +
414B ILE* 4.2 1.6 - - - -
421B VAL* 4.1 6.3 - - + -
422B PRO 3.5 4.5 - - - +
423B CYS* 2.0 46.0 - - - -
444B ILE* 3.7 15.7 - - - -
445B TYR* 1.3 73.8 - - - +
447B LEU* 1.3 71.4 - - - +
448B MET* 3.3 16.2 + - + +
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Residues in contact with LEU 447 (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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209A TYR 4.5 2.9 - - - +
86B CYS* 3.6 25.4 - - + +
87B GLN 4.6 1.8 - - - +
88B GLY* 3.9 18.6 - - - +
89B SER 3.9 2.9 - - - +
90B THR 3.3 28.7 - - - +
91B PHE* 3.7 21.2 - - + -
354B GLN* 3.7 21.1 - - + +
363B TRP* 4.0 9.9 - - + +
421B VAL* 3.7 16.3 - - - +
422B PRO* 2.9 43.3 + - + +
446B CYS* 1.3 71.4 - - - +
448B MET* 1.3 63.2 + - - +
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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