Contacts of the strand formed by residues 284 - 289 (chain A) in PDB entry 4KPF
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 ILE 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ILE* 4.8 3.6 - - + +
275A VAL* 3.7 32.1 - - + -
276A ARG* 3.4 46.9 + - + +
279A ASN* 5.3 2.9 + - - +
281A VAL* 4.7 8.0 + - + +
282A ALA 3.8 0.2 - - - -
283A GLY* 1.3 76.1 - - - +
285A ALA* 1.3 61.9 + - - +
286A GLU 4.1 2.5 - - - +
287A VAL* 4.1 8.5 - - + -
300A ILE* 3.8 22.2 - - + -
301A GLU 4.1 1.6 - - - -
302A LEU* 4.2 4.0 - - + -
303A LYS* 3.5 13.6 + - - -
311A VAL* 4.1 30.5 - - + -
315A LEU* 4.4 12.1 - - + -
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LYS* 6.4 0.2 - - + -
276A ARG* 3.7 14.1 + - - -
283A GLY 3.6 1.0 + - - -
284A ILE* 1.3 75.0 - - - +
286A GLU* 1.3 62.8 + - + +
301A GLU* 2.7 35.6 + - + +
302A LEU 3.8 13.0 - - - +
303A LYS* 3.9 15.0 - - + +
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ARG* 3.8 7.8 - - - +
284A ILE* 3.7 1.0 - - - -
285A ALA* 1.3 84.0 - - + +
287A VAL* 1.3 70.4 + - - +
288A ARG* 3.5 41.3 + - + +
299A ALA 3.9 0.3 - - - +
300A ILE* 3.7 4.3 - - - +
301A GLU* 3.0 42.6 + - + +
420D GLN* 5.6 0.7 + - - +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A VAL* 3.8 33.9 - - + +
272A ILE* 3.6 30.7 - - + -
273A ASP* 3.8 35.9 + - + +
276A ARG* 4.6 0.6 - - - +
284A ILE* 4.1 14.6 - - + -
286A GLU* 1.3 81.5 - - - +
288A ARG* 1.3 65.0 + - - +
289A ASP 4.2 0.6 + - - -
298A ILE* 4.3 14.4 - - + -
299A ALA 3.7 3.8 - - - +
300A ILE* 4.5 4.9 - - + -
420D GLN* 4.9 1.9 + - - -
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLN* 2.9 31.3 + - - +
286A GLU* 3.5 35.4 + - - +
287A VAL* 1.3 74.1 - - - +
289A ASP* 1.3 62.3 + - - +
290A GLU* 2.1 53.1 + - + +
297A ARG* 5.3 0.2 - - - +
298A ILE* 3.4 4.3 - - - -
299A ALA* 2.9 40.9 + - - +
301A GLU* 2.9 31.4 + - - +
420D GLN* 3.6 23.3 - - + +
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Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 4.2 5.7 - - - +
265A LYS* 3.0 29.9 - - - +
266A ALA* 5.3 1.4 - - - -
269A VAL* 3.9 30.5 - - + +
287A VAL 4.2 1.4 + - - -
288A ARG* 1.3 70.6 - - - +
290A GLU* 1.3 57.4 + - - +
291A SER* 2.5 30.8 + - - -
297A ARG 3.6 2.9 - - - +
298A ILE* 4.2 7.5 - - - +
420D GLN* 3.4 15.4 + - - +
447D ARG* 3.2 39.7 + - - +
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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