Contacts of the strand formed by residues 3171 - 3173 (chain B) in PDB entry 1DJO
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 VAL3171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3103B LEU* 5.2 2.7 - - + -
3104B GLU* 3.4 9.0 - - + +
3107B ALA* 5.4 0.2 - - + -
3159B VAL* 3.5 18.8 - - + -
3166B GLN* 3.7 31.4 - - + +
3167B SER 3.2 20.5 + - - +
3168B GLY* 4.1 9.9 - - - +
3170B ASP* 1.3 77.0 + - - +
3172B SER* 1.3 62.8 + - - +
3182B PHE* 3.6 34.8 - - + -
3183B LYS 3.5 8.5 - - - +
3184B SER* 4.1 3.8 - - - -
3312B LYS* 2.8 25.1 + - - +
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Residues in contact with SER3172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1282A HIS 5.6 0.9 + - - -
3104B GLU* 2.8 28.4 + - - -
3170B ASP 4.4 4.5 - - - -
3171B VAL* 1.3 75.3 - - - +
3173B LYS* 1.3 66.4 + - - +
3174B SER* 2.9 24.1 + - - -
3182B PHE* 3.4 6.6 - - - -
3183B LYS 2.8 23.3 + - - -
3284B ASN 6.2 0.4 - - - -
3309B ASN* 3.5 17.5 + - - -
3311B GLU* 4.2 2.3 + - - -
3312B LYS* 4.7 0.2 - - - -
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Residues in contact with LYS3173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255A GLY* 3.6 21.9 - - - +
1256A ASN 4.7 1.2 - - - +
1282A HIS* 4.2 4.7 + - + +
1283A VAL* 3.5 29.0 - - + +
3100B THR* 2.7 38.9 + - - +
3101B ASP* 2.7 28.9 + - - +
3104B GLU* 3.0 19.5 + - - +
3126B MET* 3.6 30.0 - - - +
3172B SER* 1.3 74.4 + - - +
3174B SER* 1.3 58.2 + - - +
3175B ILE 4.7 0.4 - - - -
3176B ASN* 4.1 6.6 + - - -
3181B ALA* 3.6 10.5 - - + -
3182B PHE* 3.8 23.1 - - + -
4000B CAB 4.3 6.1 + - - -
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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
------------------------------------------------------------
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