Contacts of the helix formed by residues 860 - 865 (chain B) in PDB entry 4UN5
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 860 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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837B ASP* 3.6 7.5 + - - -
858B THR* 3.7 10.1 + - - +
859B ARG* 1.3 81.8 - - - +
861B ASP* 1.3 59.2 + - - +
862B LYS* 3.1 21.5 + - - +
863B ASN* 3.1 38.3 + - - +
864B ARG 4.4 0.5 + - - -
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Residues in contact with ASP 861 (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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837B ASP* 3.4 26.6 + - + +
839B ASP* 4.2 27.6 - - + +
858B THR* 3.8 8.8 - - - +
860B SER* 1.3 69.6 + - - +
862B LYS* 1.3 75.8 + - - +
863B ASN 3.1 0.7 - - - -
864B ARG* 3.2 30.2 + - - +
865B GLY 4.8 0.2 - - - +
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Residues in contact with LYS 862 (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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860B SER* 3.1 12.9 - - - +
861B ASP* 1.3 88.6 + - - +
863B ASN* 1.3 60.9 + - - +
864B ARG 3.1 6.8 + - - -
865B GLY* 3.4 18.6 + - - +
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Residues in contact with ASN 863 (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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823B TYR* 4.1 11.9 - - + +
824B VAL* 4.1 29.3 - - + +
826B GLN* 5.9 0.4 - - - +
859B ARG* 5.2 3.8 - - - +
860B SER* 3.1 32.6 + - - +
862B LYS* 1.3 78.4 - - - +
864B ARG* 1.3 61.7 + - - +
865B GLY 3.1 2.6 + - - -
875B VAL* 3.6 15.9 - - - +
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Residues in contact with ARG 864 (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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823B TYR* 3.6 31.0 - - + -
839B ASP* 2.7 28.9 + - - +
840B ALA 3.0 13.0 + - - -
841B ILE* 2.7 30.5 + - - +
843B PRO* 4.1 6.4 - - - +
861B ASP* 3.2 23.3 + - - +
862B LYS 3.1 0.8 - - - -
863B ASN* 1.3 77.9 - - - +
865B GLY* 1.3 62.8 + - - +
866B LYS 2.6 36.6 + - - +
867B SER* 3.8 17.5 + - - +
869B ASN 2.7 21.6 + - - -
871B PRO* 3.4 21.8 - - + +
872B SER 3.2 21.5 + - - -
875B VAL* 3.8 7.9 - - - +
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Residues in contact with GLY 865 (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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861B ASP 4.8 0.3 - - - +
862B LYS* 3.4 15.4 + - - +
863B ASN 3.1 5.1 + - - -
864B ARG* 1.3 82.7 - - - +
866B LYS* 1.3 68.5 + - - -
867B SER* 3.8 1.2 + - - -
872B SER* 4.0 14.4 - - - -
875B VAL* 5.2 0.7 - - - -
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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