Contacts of the helix formed by residues 297 - 306 (chain G) in PDB entry 2F1U
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 297 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A VAL* 5.0 8.3 - - + -
264F CYS* 3.6 14.8 - - + -
293G LEU 4.6 2.2 - - - +
294G THR* 2.9 35.5 + - + +
296G MET* 1.3 75.9 - - - +
298G SER* 1.3 63.7 + - - +
300G CYS* 3.1 11.9 - - - -
301G VAL* 2.8 50.7 + - + +
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Residues in contact with SER 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C SER* 5.6 0.6 + - - -
260F ALA 5.3 0.2 - - - -
261F PHE* 4.5 11.2 - - - -
264F CYS* 3.4 22.0 - - - -
265F TRP* 2.7 32.2 + - - -
295G ALA 2.8 11.7 + - - -
297G ILE* 1.3 78.2 - - - +
299G THR* 1.3 60.0 + - - +
300G CYS 2.8 13.3 + - - -
301G VAL* 3.3 12.3 - - - -
302G ASN* 3.1 40.4 + - - +
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Residues in contact with THR 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 4.8 4.5 - - - +
51A GLY* 4.1 5.0 - - - -
55A ASN* 3.7 2.6 - - - +
79B LEU* 5.1 0.2 - - - -
83B ASP* 2.9 36.0 - - - +
86B VAL* 3.7 21.1 - - + +
91B LEU* 5.1 1.2 - - - +
117C GLN* 5.0 2.8 - - + +
120C SER* 3.3 28.0 - - - +
124C SER* 5.2 2.9 - - - +
261F PHE* 6.6 0.2 - - + -
265F TRP* 4.6 11.0 - - + -
296G MET* 2.6 35.7 + - - +
297G ILE 3.7 1.6 - - - -
298G SER* 1.3 78.6 + - - +
300G CYS* 1.3 62.7 + - - +
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Residues in contact with CYS 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 5.1 5.4 - - - +
50A LEU* 3.6 36.9 - - + +
51A GLY* 3.6 22.0 - - - -
54A GLY* 5.9 2.0 - - - -
55A ASN* 3.4 11.4 + - - +
83B ASP* 3.2 5.2 + - - -
296G MET 4.3 2.2 - - - -
297G ILE* 3.1 25.4 - - - -
298G SER 2.8 7.3 + - - -
299G THR* 1.3 75.5 - - - +
301G VAL* 1.3 64.9 + - - +
302G ASN 3.3 1.3 - - - -
303G PRO* 3.1 19.5 - - - +
304G ILE* 3.4 14.0 - - - +
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Residues in contact with VAL 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 6.0 1.1 - - + -
260F ALA* 5.0 4.9 - - + -
264F CYS* 5.8 0.4 - - + -
297G ILE* 2.8 55.9 + - + +
298G SER* 3.3 17.3 - - - -
300G CYS* 1.3 74.4 - - - +
302G ASN* 1.3 61.6 + - - +
304G ILE* 2.7 42.2 + - + +
305G PHE* 2.8 37.1 + - + -
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Residues in contact with ASN 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ILE* 4.1 5.9 - - + +
79B LEU* 3.4 33.2 - - + +
124C SER* 3.6 16.4 + - - -
128C LEU* 5.9 0.6 - - - +
257F ILE* 3.5 38.5 - - + +
260F ALA* 4.5 5.4 - - - +
261F PHE* 4.7 4.8 + - - +
298G SER* 3.1 29.3 + - - +
301G VAL* 1.3 78.2 - - - +
303G PRO* 1.3 59.4 - - + +
305G PHE* 3.1 8.3 + - - +
306G TYR* 2.8 32.6 + - - +
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Residues in contact with PRO 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLY* 4.9 7.4 - - - +
55A ASN* 3.0 32.5 - - - +
58A LEU* 3.3 30.4 - - + +
76B ILE* 3.8 4.9 - - + -
79B LEU* 5.2 0.4 - - + -
80B SER* 3.7 11.4 - - - +
83B ASP* 4.0 2.0 - - - +
300G CYS* 3.1 18.8 - - - +
302G ASN* 1.3 95.0 - - + +
304G ILE* 1.3 52.8 + - + +
306G TYR* 2.8 32.9 - - + +
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Residues in contact with ILE 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.5 17.9 - - + -
300G CYS 3.4 12.6 - - - +
301G VAL* 2.7 44.4 + - + +
303G PRO* 1.3 69.9 - - + +
305G PHE* 1.3 61.3 + - + +
306G TYR* 3.0 12.2 - - - +
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Residues in contact with PHE 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253F MET* 3.4 19.4 - - - +
256F SER* 3.6 34.8 - - - -
257F ILE* 3.4 17.3 - - + -
260F ALA* 3.3 31.2 - - + -
301G VAL* 2.8 47.0 + - + -
302G ASN* 3.3 8.5 - - - +
304G ILE* 1.3 76.5 - - + +
306G TYR* 1.3 62.4 + - - +
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Residues in contact with TYR 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.5 38.6 - - + -
62A ILE* 4.2 5.9 - - + +
72B THR* 4.3 12.8 - - + -
73B ASN* 2.7 34.4 + - - -
76B ILE* 3.5 34.0 - - + +
253F MET* 3.5 37.1 - - + +
254F LEU* 5.6 0.4 - - + -
257F ILE* 4.4 6.8 - - + +
302G ASN 2.8 13.9 + - - +
303G PRO* 2.8 25.8 - - + +
304G ILE* 3.0 12.0 - - - +
305G PHE* 1.3 78.5 - - - +
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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