Contacts of the strand formed by residues 408 - 411 (chain B) in PDB entry 2NUP
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 408 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B CYS* 3.6 3.9 - - - -
389B THR* 3.1 39.0 + - - +
407B LEU* 1.3 78.4 - - - +
409B LEU* 1.3 65.3 + - - -
787B VAL 2.8 16.4 - - - -
789B MET* 3.7 10.3 - - - -
846B LEU* 3.7 7.3 - - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PHE* 3.4 31.9 - - + -
387B ARG 3.2 7.9 - - - +
388B CYS* 3.7 33.2 - - + -
408B GLY* 1.3 73.7 - - - -
410B LEU* 1.3 68.2 + - - +
411B LEU* 3.9 5.6 - - + +
751B ILE* 4.5 13.0 - - + -
759B ILE* 5.3 0.4 - - + -
786B ALA* 3.2 3.5 - - - -
787B VAL* 2.7 42.2 + - + +
789B MET* 3.9 18.8 - - + -
803B PHE* 3.8 35.0 - - + -
823B LEU* 4.1 5.2 - - + -
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU 4.2 0.5 - - - +
386B PHE* 3.7 2.4 - - - -
387B ARG* 2.9 41.8 + - + +
389B THR* 4.2 13.7 - - + -
408B GLY 4.5 0.2 - - - +
409B LEU* 1.3 84.6 - - - +
411B LEU* 1.3 63.7 + - - +
785B TYR 3.3 6.1 - - - +
786B ALA* 4.2 13.5 - - + -
842B ALA* 4.0 27.1 - - + +
845B GLY* 4.4 3.6 - - - -
846B LEU* 4.3 16.6 - - + +
849B ASN* 6.1 0.7 - - - +
935B LEU* 3.3 44.9 - - + +
938B LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B LEU 3.3 10.5 - - - +
386B PHE* 4.1 20.6 - - + -
409B LEU* 3.9 10.5 - - + +
410B LEU* 1.3 88.5 - - - +
412B HIS* 1.3 61.1 + - - +
413B PRO* 3.2 11.0 - - + +
749B MET* 4.1 14.8 - - + -
751B ILE* 3.4 32.8 - - + -
784B GLY* 3.6 3.6 - - - -
785B TYR* 2.8 57.1 + - + +
786B ALA* 4.6 1.8 - - - +
787B VAL* 4.9 6.7 - - + +
805B SER* 4.0 15.9 - - - +
821B HIS* 6.5 0.2 - - + -
934B PRO* 5.4 2.0 - - - +
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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