Contacts of the strand formed by residues 278 - 283 (chain A) in PDB entry 4IX8
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 ARG 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ILE* 4.5 7.4 - - - -
250A LEU* 3.1 23.3 - - + +
269A VAL* 2.7 61.1 + - + -
270A ALA* 3.8 16.6 + - - +
272A PHE 4.0 7.5 + - - -
274A THR* 3.1 43.7 + - - +
276A VAL* 2.9 21.7 + - + +
277A PRO* 1.3 78.3 - - - +
279A LEU* 1.3 59.3 + - - +
280A ILE* 4.0 1.7 - - + +
299A ILE 3.5 2.4 - - - +
300A LEU* 3.5 5.2 - - - +
301A ILE* 2.9 65.9 + - + +
303A PRO* 4.0 6.3 - - - +
310A TRP* 5.3 0.4 - - - -
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Residues in contact with LEU 279 (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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157A ALA* 3.2 34.5 - - + -
250A LEU 2.8 11.1 + - - +
251A ILE* 3.4 10.5 - - + +
252A SER* 2.9 25.2 + - - -
278A ARG* 1.3 72.3 - - - +
280A ILE* 1.3 62.3 + - - +
281A LEU* 3.8 17.0 + - + -
298A SER* 4.0 12.6 - - - +
299A ILE 3.5 19.7 - - - -
300A LEU* 3.9 11.0 - - + +
310A TRP* 3.6 29.5 - - + -
314A MET* 3.6 28.7 - - + -
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TRP* 3.6 37.2 - - + +
252A SER 3.4 6.7 - - - +
254A GLU* 3.7 8.1 - - - +
268A SER* 3.8 5.4 - - - +
269A VAL* 3.5 29.8 - - + -
270A ALA* 3.7 29.8 - - + -
278A ARG* 4.9 1.1 - - + +
279A LEU* 1.3 73.4 - - - +
281A LEU* 1.3 68.6 + - - +
282A GLY 4.2 0.6 + - - +
297A TRP* 3.9 0.6 - - - +
298A SER* 3.2 4.9 - - - -
299A ILE* 2.8 46.0 + - + +
301A ILE* 3.8 15.0 - - + -
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Residues in contact with LEU 281 (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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150A VAL* 3.9 16.4 - - + -
153A ALA* 4.1 10.5 - - + +
154A ILE* 3.7 26.0 - - + +
157A ALA* 5.2 1.3 - - + -
178A TYR* 3.6 23.3 - - + +
251A ILE* 4.0 20.0 - - + -
252A SER 2.9 11.1 + - - +
253A ASP* 3.7 6.2 - - + -
254A GLU* 2.8 31.4 + - - +
255A ILE 3.6 0.7 + - - -
279A LEU* 4.0 18.8 - - + -
280A ILE* 1.3 82.8 - - - +
282A GLY* 1.3 58.6 + - - +
297A TRP 3.5 4.0 - - - +
298A SER* 3.6 20.4 - - - -
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Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TRP* 4.5 5.8 - - - -
150A VAL* 3.4 16.5 - - - +
254A GLU 4.4 3.6 - - - -
255A ILE* 4.1 14.8 - - - -
281A LEU* 1.3 74.5 - - - +
283A GLY* 1.3 57.9 + - - -
297A TRP* 2.9 44.6 + - - +
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Residues in contact with GLY 283 (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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125A TYR* 5.3 0.9 + - - -
126A TRP* 5.0 1.2 - - - -
150A VAL* 5.0 1.1 - - - -
255A ILE* 4.2 17.2 - - - +
282A GLY* 1.3 73.5 - - - -
284A THR* 1.3 60.5 + - - -
285A ALA* 3.6 2.0 - - - -
286A LLP 5.3 0.3 + - - -
287A TYR* 3.8 15.6 - - - -
295A VAL 4.7 0.7 - - - -
296A GLY* 4.2 8.1 - - - -
297A TRP* 3.5 33.1 - - - -
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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
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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