Contacts of the strand formed by residues 239 - 246 (chain A) in PDB entry 1MS4
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 LYS 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLU* 3.5 6.0 - - - +
236A TRP* 2.9 41.2 + - - +
237A GLU* 3.8 15.3 + - - +
238A GLY* 1.3 83.9 - - - +
240A LEU* 1.3 69.1 + - - +
241A ILE* 3.5 3.8 + - + +
255A GLU* 3.4 39.1 + - + +
256A SER 3.6 10.1 - - - +
257A SER* 3.9 20.9 - - - +
324A ASN* 5.8 0.8 + - - -
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Residues in contact with LEU 240 (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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183A ILE* 3.9 27.6 - - + -
185A ALA* 5.2 0.4 - - + -
191A VAL* 4.1 20.6 - - + -
207A ILE* 3.8 25.8 - - + -
233A ALA* 5.1 3.8 - - + -
234A LEU 3.5 5.6 - - - +
235A GLU* 4.3 16.4 - - + +
239A LYS* 1.3 73.8 - - - +
241A ILE* 1.3 61.2 + - - +
242A ILE* 4.0 14.8 - - + -
255A GLU* 3.0 8.5 - - - +
256A SER* 2.7 42.0 + - - +
259A MET* 4.2 33.7 - - + +
260A GLY 4.9 0.4 - - - +
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Residues in contact with ILE 241 (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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233A ALA* 3.1 4.9 - - - +
234A LEU* 2.9 35.2 + - + -
236A TRP* 3.5 43.7 - - + +
239A LYS* 4.1 3.8 - - + +
240A LEU* 1.3 77.4 - - - +
242A ILE* 1.3 62.3 + - - +
243A ASN 4.0 0.2 - - - -
253A VAL* 3.7 24.0 - - + -
254A TYR 3.3 4.3 - - - +
255A GLU* 4.1 21.8 - - + +
266A ALA* 5.8 0.4 - - + -
270A LEU* 4.6 4.7 - - + -
289A PHE* 3.7 18.1 - - + -
300A MET* 4.1 17.9 - - + -
324A ASN* 4.3 7.6 - - - +
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Residues in contact with ILE 242 (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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193A PRO* 4.7 4.9 - - + -
207A ILE* 4.1 19.5 - - + -
231A PRO* 4.0 25.1 - - + -
232A VAL 3.5 5.4 - - - +
233A ALA* 3.9 13.0 - - + -
240A LEU* 4.1 16.6 - - + +
241A ILE* 1.3 75.3 - - - +
243A ASN* 1.3 60.4 + - - +
244A THR* 4.0 6.4 + - + -
252A LEU 4.1 0.5 - - - +
253A VAL* 3.5 4.0 - - - -
254A TYR* 2.7 44.3 + - - +
256A SER* 4.3 13.9 - - - -
263A TRP* 3.6 42.2 - - + -
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Residues in contact with ASN 243 (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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231A PRO* 3.6 0.5 - - - +
232A VAL* 2.8 40.2 + - + +
241A ILE 4.0 1.4 - - - -
242A ILE* 1.3 71.4 - - - +
244A THR* 1.3 61.8 + - - +
251A ARG* 2.8 38.3 + - - +
252A LEU 4.1 2.5 - - - -
253A VAL* 3.9 17.7 - - + +
274A TRP* 3.5 19.4 - - - -
289A PHE* 3.6 30.2 - - + -
302A PHE* 3.1 29.7 - - - -
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Residues in contact with THR 244 (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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205A SER* 4.0 12.1 - - - +
228A CYS* 3.7 35.9 - - + +
229A SER 4.0 5.4 - - - -
231A PRO* 4.3 3.4 - - + -
242A ILE* 4.2 18.4 - - + +
243A ASN* 1.3 77.6 + - - +
245A ARG* 1.3 61.1 + - - +
246A VAL* 3.9 1.7 - - - +
251A ARG* 3.3 33.3 - - - +
252A LEU 2.7 31.1 + - - +
254A TYR* 4.2 13.0 - - + -
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Residues in contact with ARG 245 (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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227A GLY 3.5 0.3 - - - +
228A CYS* 3.3 5.7 - - - -
229A SER* 2.7 59.9 + - - +
230A GLU* 2.8 37.0 + - + +
244A THR* 1.3 70.6 - - - +
246A VAL* 1.3 62.2 + - - +
247A ASP* 3.0 33.3 + - - +
251A ARG* 3.5 9.6 - - - +
284A GLY* 3.3 19.7 + - - +
285A SER* 3.2 32.8 - - - +
312A TRP* 4.1 15.0 - - - +
314A ARG* 3.6 13.5 - - - +
342A TYR* 3.1 18.4 + - - -
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Residues in contact with VAL 246 (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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226A PHE 5.5 1.3 - - - +
227A GLY* 3.8 18.6 - - - +
228A CYS* 4.2 8.5 - - - -
244A THR* 3.9 7.7 + - - +
245A ARG* 1.3 82.0 - - - +
247A ASP* 1.3 69.5 + - - +
248A TYR 3.3 0.5 + - - -
249A ARG* 3.0 43.3 + - + +
250A ARG 3.7 22.0 - - - +
251A ARG* 4.4 3.9 - - - +
252A LEU* 3.9 27.8 - - + +
276A PRO* 4.4 4.0 - - - +
284A GLY* 4.6 3.6 + - - -
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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