Contacts of the strand formed by residues 252 - 258 (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 GLU 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ILE* 3.8 20.7 - - + +
245A GLU 3.6 8.1 - - - +
246A LYS* 4.9 7.4 - - + +
247A LEU* 4.8 3.3 - - - +
250A GLY 4.3 3.8 + - - +
251A LYS* 1.3 80.8 - - - +
253A GLN* 1.3 61.6 + - - +
301A GLU* 4.0 1.7 - - - +
302A LEU* 3.0 36.7 + - + +
303A LYS 4.9 1.2 + - - -
308A THR* 3.0 39.6 + - + +
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Residues in contact with GLN 253 (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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244A ILE* 3.3 7.8 - - - +
245A GLU* 2.8 68.8 + - + +
247A LEU* 4.2 18.5 - - + +
252A GLU* 1.3 75.2 - - - +
254A ILE* 1.3 62.9 + - - +
255A VAL* 3.6 11.5 + - + +
288A ARG* 2.9 31.3 + - - +
297A ARG* 4.4 9.7 - - - +
299A ALA* 4.7 3.8 - - - +
300A ILE 3.6 8.7 - - - +
301A GLU* 3.8 26.6 - - + +
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Residues in contact with ILE 254 (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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242A THR* 4.4 13.5 - - + -
243A GLU 3.8 7.6 - - - +
244A ILE* 4.3 16.6 - - + -
253A GLN* 1.3 71.5 - - - +
255A VAL* 1.3 62.1 + - - +
256A ILE* 4.0 7.6 + - + -
298A ILE 3.5 2.1 - - - +
299A ALA* 3.6 1.0 - - - -
300A ILE* 2.8 54.2 + - + +
302A LEU* 4.1 27.1 - - + -
308A THR* 4.5 3.1 - - - +
311A VAL* 4.2 17.3 - - + -
312A LEU* 3.5 45.3 - - + +
315A LEU* 4.9 0.4 - - + -
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Residues in contact with VAL 255 (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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242A THR* 3.6 2.7 - - - -
243A GLU* 2.9 43.2 + - + +
245A GLU* 3.5 32.1 - - + +
253A GLN* 3.6 22.0 - - + +
254A ILE* 1.3 75.7 - - - +
256A ILE* 1.3 69.7 + - - +
257A THR* 3.6 15.1 - - + +
297A ARG* 3.6 32.1 - - + +
298A ILE 3.4 7.6 - - - +
299A ALA* 4.5 3.1 - - - -
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Residues in contact with ILE 256 (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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240A SER* 3.8 10.5 - - - -
241A LYS 3.5 5.6 - - - +
242A THR* 4.1 11.4 - - + -
254A ILE* 4.7 7.6 - - + +
255A VAL* 1.3 74.2 - - - +
257A THR* 1.3 63.6 + - - +
258A GLU 3.6 19.3 - - - +
259A ILE* 3.7 18.2 - - + -
272A ILE* 4.5 7.6 - - + -
296A LEU* 3.8 2.6 - - + +
297A ARG* 3.3 7.4 - - - -
298A ILE* 2.9 51.1 + - + +
300A ILE* 4.3 19.1 - - + -
321A LEU* 3.1 33.7 - - + -
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Residues in contact with THR 257 (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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241A LYS* 3.0 33.3 + - + +
243A GLU* 5.0 9.0 - - + +
255A VAL* 3.6 22.0 - - + +
256A ILE* 1.3 78.9 - - - +
258A GLU* 1.3 70.2 + - - +
296A LEU* 3.6 37.8 - - - +
297A ARG* 6.0 0.2 - - + -
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Residues in contact with GLU 258 (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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215A THR 3.7 14.1 - - - +
216A GLY* 3.4 4.8 - - - -
217A ALA* 2.4 39.6 + - - +
240A SER* 3.1 9.8 - - - -
241A LYS* 3.1 46.2 + - + +
256A ILE* 3.6 1.6 - - - +
257A THR* 1.3 92.5 + - - +
259A ILE* 1.3 66.1 + - - +
296A LEU* 4.9 2.9 - - - -
479A LEU* 3.7 11.9 - - - +
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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