Contacts of the helix formed by residues 305 - 314 (chain A) in PDB entry 1F44
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 SER 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A GLY 3.4 3.5 + - - -
304A VAL* 1.3 79.7 - - - +
306A ILE* 1.3 66.2 + - - +
307A PRO* 3.5 14.5 - - - +
308A GLU* 3.3 26.3 + - - +
309A ILE* 3.0 20.7 + - - +
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Residues in contact with ILE 306 (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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304A VAL 3.8 0.2 + - - -
305A SER* 1.3 74.0 - - - +
307A PRO* 1.3 63.8 - - + +
309A ILE* 3.1 10.8 + - + +
310A MET* 2.7 61.9 + - + +
318A VAL* 3.9 19.7 - - + -
321A VAL* 4.8 1.3 - - + -
322A MET* 3.5 40.8 - - + -
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Residues in contact with PRO 307 (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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305A SER* 3.5 15.7 - - - +
306A ILE* 1.3 97.9 - - + +
308A GLU* 1.3 58.0 + - + +
310A MET* 3.2 11.8 + - + +
311A GLN* 2.9 28.8 + - - +
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Residues in contact with GLU 308 (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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299A MET* 4.7 0.7 - - - +
304A VAL* 3.7 24.6 - - + +
305A SER* 3.3 17.5 + - - +
306A ILE 3.2 0.6 - - - -
307A PRO* 1.3 75.4 - - + +
309A ILE* 1.3 60.9 + - - +
311A GLN* 3.4 9.7 + - - +
312A ALA* 3.0 27.5 + - - +
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Residues in contact with ILE 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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299A MET* 3.8 27.6 - - + -
300A ALA* 3.9 28.3 - - + +
304A VAL* 3.6 30.3 - - + +
305A SER 3.0 17.2 + - - +
306A ILE* 3.6 17.0 - - + +
308A GLU* 1.3 72.6 - - - +
310A MET* 1.3 66.7 + - - +
312A ALA* 3.2 10.6 + - - +
313A GLY 3.2 9.7 + - - -
315A TRP* 3.6 8.4 - - + -
321A VAL* 3.9 22.9 - - + -
322A MET* 5.3 4.3 - - + -
325A ILE* 4.1 16.6 - - + -
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Residues in contact with MET 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 ILE* 2.7 48.1 + - - +
307A PRO* 3.5 9.2 - - + +
309A ILE* 1.3 74.9 - - - +
311A GLN* 1.3 57.5 + - - +
313A GLY 3.4 0.2 + - - -
314A GLY* 2.8 26.7 + - - -
315A TRP* 2.8 32.4 + - + +
316A THR* 3.3 37.7 - - - +
317A ASN 3.5 16.4 - - - +
318A VAL* 3.6 13.9 - - + +
321A VAL* 3.8 20.0 - - + -
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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
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211A LYS* 3.9 7.6 + - - -
307A PRO 2.9 16.5 + - - +
308A GLU* 3.8 9.5 - - - +
310A MET* 1.3 77.6 - - - +
312A ALA* 1.3 61.9 + - - +
313A GLY 3.3 0.5 + - - -
314A GLY* 3.4 9.8 + - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A ASN 5.2 1.1 - - - +
170A THR 3.4 9.9 - - - +
171A LEU* 3.9 11.4 - - + +
211A LYS* 2.9 19.7 + - - +
299A MET* 3.4 37.2 - - + -
308A GLU 3.0 13.4 + - - +
309A ILE 3.2 3.1 + - - +
311A GLN* 1.3 77.0 - - - +
313A GLY* 1.3 57.3 + - - +
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Residues in contact with GLY 313 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A THR 4.8 0.2 - - - -
171A LEU* 4.0 5.8 - - - -
211A LYS* 4.5 4.0 - - - -
292A ARG* 3.0 37.5 + - - -
309A ILE 3.2 9.3 + - - -
311A GLN 3.2 0.2 - - - -
312A ALA* 1.3 77.0 - - - +
314A GLY* 1.3 60.3 + - - +
315A TRP* 3.4 23.9 - - - -
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Residues in contact with GLY 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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209A VAL* 6.5 1.1 - - - -
211A LYS* 4.6 3.2 - - - +
292A ARG* 5.1 0.4 - - - -
310A MET 2.8 10.3 + - - -
311A GLN* 3.4 9.3 + - - -
313A GLY* 1.3 78.6 - - - +
315A TRP* 1.3 60.5 + - - -
316A THR* 3.9 7.4 + - - +
16M C 5.6 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