Contacts of the helix formed by residues 249 - 259 (chain A) in PDB entry 6S1M
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 ASP 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A VAL* 1.3 78.4 - - - +
250A PHE* 1.3 72.8 + - - +
251A GLU* 3.6 13.1 - - - +
252A ILE* 3.4 20.8 + - + +
253A ARG* 2.8 36.5 + - - +
545A TYR* 3.4 22.4 + - - -
549A ARG* 4.8 7.8 + - - -
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Residues in contact with PHE 250 (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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103A HIS* 3.3 36.6 - + + -
123A PRO* 4.3 5.6 - - + -
125A LEU* 3.9 29.2 - - + -
144A PHE* 3.5 41.1 - + - -
146A PRO* 4.1 25.4 - - + -
217A PRO* 3.7 29.8 - - + -
248A VAL 4.0 1.0 + - - -
249A ASP* 1.3 81.9 + - - +
251A GLU* 1.3 67.7 + - + +
253A ARG* 3.1 8.6 + - + +
254A PHE* 2.9 25.8 + - + +
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Residues in contact with GLU 251 (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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101A ILE* 3.7 34.9 - - + -
102A ASP* 4.2 6.8 - - - +
103A HIS* 3.4 32.9 + - - +
125A LEU* 5.4 9.6 - - + -
249A ASP* 3.6 16.4 + - - +
250A PHE* 1.3 84.1 - - + +
252A ILE* 1.3 61.6 + - + +
254A PHE* 3.3 8.6 + - - +
255A MET* 3.0 35.5 + - - +
542A PRO* 6.0 0.4 - - + -
545A TYR* 5.3 6.4 + - - +
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Residues in contact with ILE 252 (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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248A VAL* 5.5 3.6 - - + -
249A ASP* 3.7 27.1 - - + +
250A PHE 3.2 0.8 - - - -
251A GLU* 1.3 78.6 - - + +
253A ARG* 1.3 55.9 - - - +
255A MET* 3.8 7.3 - - + +
256A VAL* 2.9 46.7 + - + +
540A GLY 5.6 2.0 - - - +
541A VAL* 5.4 5.6 - - + -
542A PRO* 4.1 18.6 - - + -
545A TYR* 3.6 35.0 - - + +
553A VAL* 5.9 0.7 - - + +
556A VAL* 6.1 2.9 - - + -
557A SER* 4.7 18.8 - - - +
560A LEU* 5.5 8.1 - - + -
561A ARG* 6.2 1.1 - - - +
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Residues in contact with ARG 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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144A PHE* 4.6 7.2 - - + -
146A PRO* 6.0 2.2 - - + -
147A TYR* 3.8 44.0 + - + +
149A TYR* 5.3 4.2 - - - -
246A ALA* 4.3 22.2 + - - +
248A VAL* 3.8 26.6 - - + +
249A ASP 2.8 19.4 + - - +
250A PHE* 3.4 9.0 - - + +
252A ILE* 1.3 74.2 - - - +
254A PHE* 1.3 58.7 + - - +
256A VAL* 3.7 17.0 - - - +
257A ASP* 2.9 50.2 + - - +
560A LEU* 5.0 16.9 + - - +
564A MET* 3.4 28.9 - - - +
569A LEU* 5.9 0.6 - - - +
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Residues in contact with PHE 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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101A ILE* 6.3 3.4 - - + -
125A LEU* 3.6 33.9 - - + -
141A ILE* 4.1 29.4 - - + -
144A PHE* 3.7 43.2 - + + -
250A PHE* 2.9 13.8 + - + +
251A GLU* 3.3 13.0 + - - +
253A ARG* 1.3 76.8 - - - +
255A MET* 1.3 60.8 + - + +
257A ASP* 3.2 3.6 + - - +
258A THR* 3.0 41.6 + - + +
260A ILE* 3.6 28.3 - - + -
292A TRP* 4.4 21.5 - + + -
295A VAL* 6.0 4.5 - - + -
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Residues in contact with MET 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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98A GLN* 5.0 5.8 - - - +
101A ILE* 3.6 27.4 - - + -
251A GLU 3.0 24.1 + - - +
252A ILE* 4.0 8.1 - - - +
254A PHE* 1.3 76.0 - - + +
256A VAL* 1.3 64.9 + - - +
259A ASP* 3.2 20.1 + - - -
260A ILE* 3.3 52.0 + - + +
261A VAL* 4.1 21.1 - - - +
262A GLY* 4.3 2.7 - - - +
540A GLY 4.4 5.4 - - - +
542A PRO* 3.8 32.3 - - + -
561A ARG* 3.6 11.4 + - - +
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Residues in contact with VAL 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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252A ILE* 2.9 33.1 + - + +
253A ARG* 3.7 30.3 - - - +
255A MET* 1.3 73.8 - - - +
257A ASP* 1.3 63.8 + - - +
259A ASP* 3.6 13.5 - - - +
557A SER* 4.6 2.9 - - - +
560A LEU* 4.3 32.8 - - + +
561A ARG* 4.0 34.6 + - + +
564A MET* 4.1 17.0 - - + +
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Residues in contact with ASP 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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144A PHE* 3.2 29.4 - - + -
147A TYR* 3.6 24.5 + - - -
253A ARG* 2.9 30.4 + - - +
254A PHE* 3.2 7.8 + - - +
256A VAL* 1.3 80.0 - - - +
258A THR* 1.3 68.6 + - + +
259A ASP* 3.6 3.5 + - - +
292A TRP* 4.6 6.0 - - + -
564A MET* 4.1 17.5 - - - +
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Residues in contact with THR 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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254A PHE* 3.0 27.9 + - + +
257A ASP* 1.3 84.6 - - + +
259A ASP* 1.3 68.2 + - - +
260A ILE* 3.4 30.5 + - - +
292A TRP* 4.3 31.2 - - + +
295A VAL* 5.1 12.1 - - + +
297A SER* 4.2 6.9 - - - -
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Residues in contact with ASP 259 (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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255A MET 3.2 9.2 + - - +
256A VAL 3.6 13.0 - - - +
257A ASP 4.2 2.8 - - - +
258A THR* 1.3 79.4 - - - +
260A ILE* 1.3 60.0 + - - +
261A VAL* 4.2 4.5 + - - +
264A ASN* 4.1 1.4 + - - -
297A SER* 2.9 20.3 + - - +
561A ARG* 4.3 13.4 + - - +
565A HIS* 5.1 11.8 + - - -
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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