Contacts of the strand formed by residues 208 - 217 (chain A) in PDB entry 1MKM
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 PRO 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LYS* 3.8 6.8 - - - +
139A ILE* 3.4 51.0 - - - +
142A PHE* 3.8 25.1 - - + +
143A VAL* 3.7 20.2 - - + +
200A PRO* 4.5 5.8 - - + -
201A ILE 3.5 9.4 - - - +
202A PHE* 4.1 7.4 - - + -
206A GLY 3.8 6.7 - - - +
207A TYR* 1.3 91.8 - - + +
209A VAL* 1.3 64.5 + - - +
210A ALA 3.1 4.4 + - - -
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Residues in contact with VAL 209 (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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77A ILE* 3.8 25.8 - - + -
100A LEU* 3.6 8.9 - - + +
101A LYS* 3.1 27.5 + - - +
201A ILE* 3.1 14.3 + - + +
203A ASP* 3.5 26.2 - - + +
207A TYR* 2.8 30.8 + - + +
208A PRO* 1.3 72.2 - - - +
210A ALA* 1.3 64.9 + - + +
244A LEU* 4.0 16.6 - - + -
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Residues in contact with ALA 210 (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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77A ILE* 4.9 4.9 - - + -
98A LEU* 4.0 14.8 - - + -
99A ILE 2.8 24.0 - - - +
100A LEU* 4.0 8.5 - - + -
139A ILE* 3.9 15.2 - - - +
200A PRO* 3.3 4.5 - - - +
201A ILE* 2.5 44.2 + - + +
208A PRO 3.1 3.1 - - - -
209A VAL* 1.3 87.8 - - + +
211A GLY* 1.3 52.4 + - - +
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Residues in contact with GLY 211 (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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97A HIS 3.8 0.3 - - - +
98A LEU* 3.6 1.7 - - - -
99A ILE 2.9 33.1 + - - -
135A SER* 3.8 19.8 - - - -
138A SER* 4.2 3.4 - - - -
139A ILE* 4.0 2.8 - - - +
199A VAL 3.1 12.8 - - - -
200A PRO* 4.1 1.8 - - - -
201A ILE* 4.2 3.8 - - - -
210A ALA* 1.3 77.1 - - - +
212A VAL* 1.3 62.9 + - - -
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Residues in contact with VAL 212 (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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85A LEU* 3.3 33.7 - - + -
88A ILE* 4.4 12.1 - - + -
96A VAL* 4.4 4.7 - - + -
97A HIS 3.3 15.9 - - - +
98A LEU* 4.2 9.2 - - + -
135A SER* 4.7 0.4 - - - -
198A GLY* 3.2 1.9 - - - -
199A VAL* 2.9 47.0 + - + +
201A ILE* 3.9 18.8 - - + -
211A GLY* 1.3 76.4 - - - +
213A SER* 1.3 60.9 + - - +
233A LEU* 4.1 10.3 - - + +
236A LYS 5.8 0.2 - - - -
237A ALA* 4.3 10.1 - - + -
240A ILE* 5.0 3.6 - - + -
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Residues in contact with SER 213 (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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96A VAL* 3.3 10.9 - - - +
97A HIS* 3.1 41.5 + - - +
99A ILE* 4.5 0.7 - - - +
133A THR* 5.4 0.9 + - - -
134A ALA* 4.6 2.9 - - - -
135A SER* 4.1 19.9 + - - -
196A CYS* 4.7 4.3 - - - +
197A VAL 2.9 19.1 - - - -
198A GLY* 3.6 7.2 - - - -
212A VAL* 1.3 77.7 - - - +
214A ILE* 1.3 64.9 + - - +
215A SER* 4.8 5.8 + - - -
233A LEU* 4.2 3.8 - - - +
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Residues in contact with ILE 214 (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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88A ILE* 4.2 11.7 - - + -
92A THR* 4.1 18.6 - - + +
94A GLU* 3.4 36.6 - - + +
95A THR 3.7 4.0 - - - +
96A VAL* 4.5 2.0 - - + -
195A MET 3.7 0.5 - - - +
196A CYS* 3.0 25.2 - - - +
197A VAL* 2.9 12.4 + - + +
213A SER* 1.3 74.2 - - - +
215A SER* 1.3 60.8 + - - +
221A PHE* 3.8 12.7 - - + -
229A TYR* 3.7 39.0 - - + +
232A VAL* 4.7 0.9 - - + -
233A LEU* 3.3 31.9 - - + -
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Residues in contact with SER 215 (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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94A GLU* 3.7 14.7 - - - +
95A THR* 3.2 34.5 + - - +
97A HIS* 4.2 8.8 + - - -
118A ILE* 5.0 2.5 - - - +
120A MET* 3.9 26.5 - - - +
194A ILE* 4.4 2.2 - - - -
195A MET 3.4 3.8 - - - -
196A CYS* 2.6 27.8 - - - +
213A SER* 4.2 3.5 + - - -
214A ILE* 1.3 74.2 - - - +
216A GLY* 1.3 58.7 + - - +
221A PHE* 4.1 2.7 - - - -
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Residues in contact with GLY 216 (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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94A GLU* 3.8 12.3 - - - -
118A ILE* 4.1 11.4 - - - -
120A MET* 6.3 0.4 - - - -
194A ILE* 3.4 8.2 - - - +
195A MET 2.9 32.7 + - - +
215A SER* 1.3 75.5 - - - +
217A VAL* 1.3 64.7 + - - -
221A PHE* 3.5 14.4 - - - -
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Residues in contact with VAL 217 (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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118A ILE* 3.3 32.0 - - + +
193A GLY* 3.4 14.4 - - - +
194A ILE* 4.6 1.3 - - + +
216A GLY* 1.3 68.6 - - - -
218A ALA* 1.3 71.6 + - + +
219A ARG* 3.4 42.8 - - + +
220A LYS* 2.8 40.1 + - - +
221A PHE* 3.7 2.3 - - - -
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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