Contacts of the helix formed by residues 308 - 318 (chain A) in PDB entry 1MF7
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 ILE 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A PHE* 4.0 9.0 - - + -
269A ILE* 3.9 36.8 - - + -
297A PHE* 3.9 40.2 - - + -
298A GLN 5.7 0.4 - - - +
299A VAL* 3.9 18.2 - - + -
305A LEU* 3.2 17.0 - - + +
307A THR* 1.3 92.2 - - - +
309A GLN* 1.3 63.5 + - - +
310A ASN 3.3 2.9 + - - -
311A GLN* 3.4 15.6 + - + +
312A LEU* 3.0 23.5 + - + +
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Residues in contact with GLN 309 (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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155A GLU* 6.0 0.9 - - - +
156A PHE* 3.5 40.5 - - + -
159A THR* 3.6 33.4 - - - +
160A VAL* 3.9 13.2 - - + +
163A GLN* 3.9 20.7 - - - +
306A LYS* 3.3 33.1 + - - +
307A THR 3.6 0.6 - - - -
308A ILE* 1.3 76.9 - - - +
310A ASN* 1.3 58.4 + - - +
312A LEU* 3.4 2.2 + - - +
313A ARG* 3.0 29.2 + - - +
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Residues in contact with ASN 310 (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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306A LYS 5.1 0.4 + - - -
307A THR 5.1 1.0 + - - -
308A ILE 3.4 0.6 - - - -
309A GLN* 1.3 76.5 - - - +
311A GLN* 1.3 63.6 + - + +
313A ARG* 3.0 37.9 - - - +
314A GLU* 2.9 56.2 + - - +
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Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PHE* 4.1 21.9 - - + -
307A THR 4.2 15.2 + - - +
308A ILE* 3.4 16.9 + - - +
309A GLN 3.3 0.2 - - - -
310A ASN* 1.3 82.3 - - + +
312A LEU* 1.3 62.7 + - - +
314A GLU* 3.4 4.9 + - - +
315A LYS* 3.1 35.3 + - - +
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Residues in contact with LEU 312 (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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137A PHE* 4.8 1.1 - - + -
156A PHE* 4.0 25.8 - - + -
160A VAL* 4.0 20.0 - - + -
238A VAL* 4.3 15.0 - - + -
267A TYR* 4.3 20.9 - - + -
269A ILE* 4.3 11.2 - - + -
297A PHE* 3.7 30.7 - - + -
308A ILE* 3.0 20.1 + - + +
309A GLN* 3.9 3.6 - - - +
311A GLN* 1.3 76.3 - - - +
313A ARG* 1.3 64.8 + - - +
315A LYS* 3.3 3.8 + - - +
316A ILE* 3.0 42.8 + - + +
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Residues in contact with ARG 313 (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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160A VAL* 5.5 3.5 - - + +
163A GLN* 2.8 67.4 + - + +
164A LEU* 3.8 30.4 - - + +
309A GLN* 3.0 15.8 + - - +
310A ASN* 3.0 41.8 - - - +
312A LEU* 1.3 78.8 - - - +
314A GLU* 1.3 64.8 + - - +
316A ILE 3.3 0.7 + - - -
317A PHE* 2.8 36.7 + - + +
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Residues in contact with GLU 314 (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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310A ASN* 2.9 46.5 + - - +
311A GLN* 3.9 5.4 - - - +
313A ARG* 1.3 83.9 - - - +
315A LYS* 1.3 64.3 + - + +
317A PHE* 4.3 5.5 - - - +
318A CYS* 3.0 41.7 + - - +
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Residues in contact with LYS 315 (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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267A TYR* 3.8 25.9 + - + +
293A ARG 4.6 5.7 + - - -
294A ASP* 3.2 38.1 + - - +
296A VAL 5.4 2.4 + - - -
297A PHE* 3.3 36.1 - - + -
311A GLN* 3.1 22.2 + - - +
312A LEU* 3.6 7.6 - - - +
314A GLU* 1.3 76.5 - - + +
316A ILE* 1.3 65.7 + - - +
318A CYS* 3.7 2.7 - - - -
319A ILE* 3.3 23.9 + - - +
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Residues in contact with ILE 316 (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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133A SER* 5.3 4.0 + - - -
135A ILE* 3.5 23.1 - - + -
137A PHE* 5.7 0.2 - - + -
160A VAL* 5.4 1.3 - - + -
164A LEU* 3.4 37.2 - - + -
166A LYS* 5.6 2.1 + - - +
236A ILE* 4.3 19.4 - - + +
238A VAL* 4.0 27.4 - - + -
267A TYR* 4.1 18.8 - - + -
312A LEU* 3.0 29.0 + - + +
313A ARG 4.0 0.4 - - - +
315A LYS* 1.3 80.3 - - - +
317A PHE* 1.3 64.3 + - - +
318A CYS 3.0 0.9 + - - -
319A ILE* 3.1 20.2 + - - +
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Residues in contact with PHE 317 (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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128A CYS* 3.7 9.2 - - + +
129A PRO 4.6 2.9 - - - +
130A GLN* 3.2 48.3 + - + +
163A GLN 4.4 9.0 - - - -
164A LEU* 3.3 27.8 - - + -
165A LYS 5.7 0.2 - - - -
166A LYS* 2.4 52.2 + - + +
313A ARG* 2.8 29.6 + - + +
314A GLU* 3.8 10.1 - - - +
316A ILE* 1.3 74.0 - - - +
318A CYS* 1.3 65.7 + - - +
319A ILE 3.8 0.3 + - - -
320A GLY 5.1 0.7 + - - -
321A SER* 4.8 0.3 + - - -
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Residues in contact with CYS 318 (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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128A CYS* 2.0 48.2 - - - -
314A GLU* 3.0 30.9 + - - +
315A LYS* 3.7 4.5 - - - +
316A ILE 3.0 1.0 - - - -
317A PHE* 1.3 81.3 - - - +
319A ILE* 1.3 57.2 + - - +
320A GLY 3.1 3.4 - - - -
321A SER 2.8 28.7 + - - +
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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