Contacts of the strand formed by residues 724 - 731 (chain B) in PDB entry 5NC5
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 724 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B ALA* 3.6 29.8 - - + -
581B GLY* 5.1 2.9 - - - +
722B GLU 3.4 10.1 - - - +
723B ASP* 1.3 77.2 - - - +
725B PRO* 1.3 79.4 + - - +
726B GLN* 4.5 2.1 + - - +
811B TYR* 3.3 10.1 - - - -
812B GLY 2.9 28.5 + - - +
814B PRO* 3.4 22.8 - - + +
23D ARG* 5.3 0.4 - - - +
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Residues in contact with PRO 725 (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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231A ASN 4.9 1.2 - - - +
232A ALA* 4.2 15.8 - - + +
233A SER 4.4 1.0 + - - -
580B ALA* 5.5 8.5 - - + +
581B GLY* 5.9 3.1 - - - +
724B THR* 1.3 97.0 + - + +
726B GLN* 1.3 62.3 + - - +
809B TRP* 4.5 6.1 - - + -
810B GLU 3.4 9.6 - - - +
811B TYR* 3.7 29.6 - - + +
23D ARG* 6.1 0.2 - - - +
44D ASP* 4.8 3.6 - - - +
46D VAL* 4.3 32.1 - - + -
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Residues in contact with GLN 726 (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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233A SER* 3.5 26.0 - - - +
235A ILE* 3.5 33.1 - - + +
53B ASP* 5.5 0.7 + - - +
55B LYS* 6.4 0.4 - - - +
84B SER* 5.2 1.2 + - - -
724B THR* 4.5 1.9 + - - +
725B PRO* 1.3 78.0 - - - +
727B PHE* 1.3 58.3 + - - +
728B LYS 3.9 0.2 + - - -
809B TRP* 3.2 13.4 - - - -
810B GLU* 2.9 56.1 + - + +
811B TYR 4.0 1.2 + - - -
812B GLY* 3.5 37.1 - - - +
813B SER 4.1 7.7 + - - +
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Residues in contact with PHE 727 (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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219A LEU* 3.7 24.9 - - + -
233A SER 2.9 15.7 + - - +
234A ILE* 4.0 17.3 - - + -
235A ILE* 2.9 31.7 + - - +
726B GLN* 1.3 72.9 - - - +
728B LYS* 1.3 59.8 + - - +
729B ILE* 3.5 18.7 + - + -
783B PRO* 4.4 23.8 - - + -
786B ILE* 4.2 27.4 - - + -
807B SER* 3.4 29.2 - - - -
808B ARG 3.9 2.2 - - - -
809B TRP* 4.1 17.5 - + + -
79D LEU* 3.7 21.5 - - + -
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Residues in contact with LYS 728 (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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235A ILE* 3.6 20.3 - - + +
236A ALA 2.7 28.3 + - - -
238A THR* 4.0 13.9 + - - +
726B GLN 3.9 1.8 + - - -
727B PHE* 1.3 72.2 - - - +
729B ILE* 1.3 63.8 + - - +
730B ASP* 3.7 23.1 + - - +
806B SER 3.8 0.2 - - - +
807B SER* 3.1 6.0 - - - -
808B ARG* 2.8 66.2 + - + +
810B GLU* 3.4 35.4 - - + +
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Residues in contact with ILE 729 (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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234A ILE* 3.6 25.8 - - + -
235A ILE 2.9 15.1 + - - +
236A ALA* 3.5 27.7 - - + +
727B PHE* 4.1 15.7 - - + -
728B LYS* 1.3 74.4 - - - +
730B ASP* 1.3 64.1 + - - +
731B ILE* 4.1 11.2 + - + +
750B LEU* 4.7 7.4 - - + -
786B ILE* 4.3 23.1 - - + -
801B PHE* 4.6 11.0 - - + -
805B SER* 3.7 28.7 - - - +
806B SER 3.3 9.0 - - - +
807B SER* 4.3 4.5 - - - +
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Residues in contact with ASP 730 (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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728B LYS* 3.7 23.0 + - - +
729B ILE* 1.3 73.3 - - - +
731B ILE* 1.3 64.9 + - - +
732B ASP* 3.6 1.4 + - - +
805B SER* 3.2 5.2 - - - -
806B SER* 2.8 49.5 + - - +
807B SER* 5.2 0.7 + - - -
808B ARG* 3.5 28.8 + - - -
145D PHE* 5.5 0.7 - - - -
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Residues in contact with ILE 731 (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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236A ALA* 5.7 6.3 - - + -
237A GLN* 4.5 18.7 - - + +
729B ILE* 4.1 11.1 + - + +
730B ASP* 1.3 75.3 - - - +
732B ASP* 1.4 67.9 + - - +
733B GLN* 3.4 30.8 + - - +
736B ALA* 5.1 0.2 - - + -
743B ILE* 4.9 6.3 - - + -
746B ILE* 4.0 44.2 - - + -
747B ASN* 4.5 5.2 - - - +
750B LEU* 5.3 5.4 - - + -
801B PHE* 4.0 17.3 - - + -
804B PHE* 3.7 8.1 - - + +
805B SER* 4.1 14.1 - - - -
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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