Contacts of the strand formed by residues 363 - 367 (chain I) in PDB entry 3KDO
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 PHE 363 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I GLY 5.4 0.4 - - - -
143I ILE* 3.8 30.6 - - + +
146I VAL* 4.0 20.2 - - + -
147I ARG* 3.8 44.6 - - + -
157I ILE* 3.9 19.5 - - + -
311I ASP 2.7 16.8 + - - +
312I GLN* 3.3 12.8 - - + -
313I LEU 3.0 22.5 + - - -
337I LEU* 5.0 0.2 - - - -
361I ALA 4.1 0.2 + - - -
362I ALA* 1.3 71.3 - - - +
364I PRO* 1.3 67.8 - - + +
365I THR* 3.5 3.5 + - - -
385I ASP* 3.3 34.3 - - - -
386I ILE* 3.4 11.7 - - - -
387I VAL* 3.6 16.4 - - + -
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Residues in contact with PRO 364 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313I LEU 3.5 7.9 - - - +
315I VAL* 4.0 7.2 - - + -
334I VAL* 4.0 29.8 - - + +
337I LEU* 4.2 14.6 - - + -
338I ARG* 3.7 25.8 - - + -
362I ALA 2.9 11.9 - - - +
363I PHE* 1.3 84.3 - - + +
365I THR* 1.3 52.3 + - - +
366I SER 4.2 0.4 - - - -
385I ASP 3.5 17.7 - - - +
386I ILE* 3.3 11.7 - - + +
387I VAL 2.7 31.9 + - - -
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Residues in contact with THR 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I TYR* 5.2 0.2 - - - +
279I HIS* 3.7 18.9 - - + -
312I GLN* 4.2 0.7 - - - +
313I LEU 2.9 17.4 + - - -
314I HIS* 3.2 38.7 - - + +
315I VAL* 3.0 26.6 + - - +
316I GLY 3.9 1.2 + - - -
363I PHE 3.5 7.4 + - - -
364I PRO* 1.3 72.9 - - - +
366I SER* 1.3 66.7 + - - +
367I SER* 3.9 3.1 + - - -
387I VAL* 3.1 32.6 - - + +
389I GLN* 4.8 6.3 - - + -
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Residues in contact with SER 366 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I VAL* 4.8 1.0 - - - +
316I GLY 2.9 20.5 + - - -
317I THR* 4.4 1.8 - - - -
364I PRO 4.2 0.8 - - - -
365I THR* 1.3 70.9 - - - +
367I SER* 1.3 61.4 + - - +
370I LEU* 3.6 11.9 - - - +
378I VAL* 3.5 12.2 - - - +
382I LEU* 3.4 22.9 - - - +
386I ILE* 4.4 5.5 - - - +
387I VAL 2.8 9.0 + - - +
388I LEU* 3.6 20.6 - - - -
389I GLN 3.1 23.7 + - - -
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Residues in contact with SER 367 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314I HIS* 3.8 22.9 - - - -
316I GLY* 4.4 1.1 + - - -
317I THR* 3.0 20.6 - - - +
323I LEU* 4.7 2.4 - - - +
365I THR* 3.9 1.8 + - - -
366I SER* 1.3 75.3 - - - +
368I GLY* 1.3 60.6 + - - +
370I LEU* 4.2 1.6 - - - -
389I GLN* 3.0 37.7 + - - +
600I CAP 2.6 44.5 + - - -
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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
------------------------------------------------------------
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