Contacts of the helix formed by residues 298 - 312 (chain A) in PDB entry 4C48
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 ASN 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A PRO* 4.1 20.1 - - + +
33A ALA* 4.6 5.2 - - + -
296A GLY 4.3 4.8 - - - +
297A ALA* 1.3 74.0 - - - +
299A ALA* 1.3 55.7 + - - +
300A LEU 3.7 1.3 - - - -
301A ASP* 3.0 32.8 + - + +
302A THR* 2.3 39.6 + - - -
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Residues in contact with ALA 299 (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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33A ALA* 3.8 16.4 - - + +
34A GLN* 5.0 15.5 - - + +
35A TYR* 5.7 3.4 - - + +
137A LEU* 3.1 33.3 - - + +
293A LEU* 4.2 14.1 - - + -
297A ALA 3.6 5.2 + - - +
298A ASN* 1.3 70.8 - - - +
300A LEU* 1.3 63.4 + - - +
302A THR* 3.1 3.5 + - - -
303A ALA* 3.0 18.9 + - - +
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Residues in contact with LEU 300 (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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32A VAL* 3.0 37.7 - - + +
33A ALA* 3.9 6.8 - - - +
34A GLN 5.6 0.2 - - - +
299A ALA* 1.3 79.0 - - - +
301A ASP* 1.3 59.7 + - - +
303A ALA* 3.4 1.7 + - - +
304A ALA* 2.8 34.4 + - + +
330A THR* 4.3 21.1 - - + -
333A VAL* 3.4 30.1 - - + -
334A LYS* 3.4 39.0 - - + +
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Residues in contact with ASP 301 (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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31A PRO* 3.5 16.0 - - - +
32A VAL* 3.3 21.6 + - - +
298A ASN* 3.0 39.8 + - + +
299A ALA 3.2 0.2 - - - -
300A LEU* 1.3 83.2 - - - +
302A THR* 1.3 56.2 + - - +
304A ALA* 3.2 8.8 + - - +
305A ALA* 2.9 28.2 + - - +
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Residues in contact with THR 302 (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 LEU* 4.8 0.9 - - + -
170A SER 3.3 24.0 + - - +
171A GLY* 3.8 25.0 - - - +
172A VAL* 4.0 10.5 - - + -
292A LYS 5.6 0.2 - - - +
293A LEU* 4.1 12.0 - - + +
297A ALA* 4.0 2.9 - - - +
298A ASN 2.3 40.6 + - - -
299A ALA* 3.4 6.4 - - - -
301A ASP* 1.3 68.5 - - - +
303A ALA* 1.3 62.3 + - - +
305A ALA* 3.1 9.8 + - - +
306A ILE* 2.9 37.2 + - + +
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Residues in contact with ALA 303 (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 LEU* 3.4 30.4 - - + +
138A MET* 4.5 9.2 - - - +
299A ALA 3.0 8.9 + - - +
300A LEU 3.7 6.5 - - - +
302A THR* 1.3 74.9 - - - +
304A ALA* 1.3 61.6 + - - +
306A ILE* 2.9 23.8 + - - +
307A ARG* 3.0 16.6 + - - +
328A ASP* 5.5 0.2 - - - +
330A THR* 3.8 19.3 - - + -
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Residues in contact with ALA 304 (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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300A LEU* 2.8 27.8 + - + +
301A ASP* 3.3 10.8 - - - +
302A THR 3.1 0.2 - - - -
303A ALA* 1.3 77.2 - - - +
305A ALA* 1.3 61.3 + - - +
307A ARG* 3.8 6.1 + - - +
308A ALA* 3.5 17.8 + - - +
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Residues in contact with ALA 305 (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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169A THR* 3.5 24.1 - - + +
170A SER 5.2 0.7 - - - +
301A ASP 2.9 13.4 + - - +
302A THR* 3.1 13.7 + - - +
304A ALA* 1.3 78.3 - - - +
306A ILE* 1.3 55.2 + - - +
308A ALA* 3.1 9.1 - - - +
309A GLU* 2.8 30.1 + - - +
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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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137A LEU* 5.1 3.1 - - + -
138A MET* 4.1 18.6 - - + -
140A VAL* 5.7 3.1 - - + -
166A ILE* 4.6 16.3 - - + +
169A THR* 5.0 5.6 - - + -
172A VAL* 4.6 9.6 - - + -
291A ILE* 3.5 51.4 - - + -
302A THR* 2.9 28.3 + - + +
303A ALA* 2.9 14.9 + - - +
305A ALA* 1.3 73.7 - - - +
307A ARG* 1.3 65.3 + - - +
308A ALA 3.1 1.6 - - - -
309A GLU* 3.6 6.4 + - - +
310A LEU* 3.1 30.2 + - + +
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Residues in contact with ARG 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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138A MET* 6.0 2.6 - - + +
303A ALA 3.0 13.8 + - - +
304A ALA* 4.1 6.5 - - - +
306A ILE* 1.3 78.0 - - - +
308A ALA* 1.3 55.9 + - - +
310A LEU* 3.8 15.7 - - - +
311A ALA* 2.9 59.0 + - + +
314A GLU* 5.5 4.6 + - - -
325A TYR* 3.9 30.8 + - - -
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Residues in contact with ALA 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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304A ALA 3.5 12.2 + - - +
305A ALA* 3.1 13.4 + - - +
306A ILE 3.1 0.2 - - - -
307A ARG* 1.3 75.7 - - - +
309A GLU* 1.3 56.0 - - - +
310A LEU 2.8 14.3 + - - -
311A ALA* 2.9 20.4 + - - +
312A LYS* 3.6 15.3 + - - +
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Residues in contact with GLU 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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165A ALA* 3.3 39.3 - - + +
166A ILE* 3.6 11.7 - - + +
168A ARG* 5.0 1.9 - - - +
169A THR* 2.2 34.3 + - - +
305A ALA 2.8 18.6 + - - +
306A ILE* 3.7 9.4 - - - +
308A ALA* 1.3 72.6 - - - +
310A LEU* 1.3 56.5 + - - +
312A LYS* 4.5 13.0 + - - +
313A MET* 3.5 18.2 - - - +
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Residues in contact with LEU 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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140A VAL* 4.3 19.3 - - + -
162A MET* 4.1 15.5 - - + -
166A ILE* 4.1 20.4 - - + -
289A LEU* 4.8 5.4 - - + -
306A ILE* 3.1 21.9 + - + +
307A ARG* 3.8 20.6 - - - +
308A ALA 2.9 1.0 - - - -
309A GLU* 1.3 75.1 - - - +
311A ALA* 1.3 66.1 + - - +
312A LYS 3.1 2.9 - - - -
313A MET* 3.1 22.1 + - - +
314A GLU* 3.8 3.6 + - - +
323A ILE* 3.5 42.0 - - + +
325A TYR* 4.5 9.0 - - + +
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Residues in contact with ALA 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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307A ARG* 2.9 41.2 + - + +
308A ALA* 2.9 9.6 + - - +
310A LEU* 1.3 77.8 - - - +
312A LYS* 1.3 56.2 + - + +
314A GLU* 2.5 33.6 - - - +
315A PRO* 4.7 0.2 - - - +
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Residues in contact with LYS 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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308A ALA 3.6 12.3 + - - +
309A GLU* 4.8 12.2 + - - +
310A LEU 3.1 1.2 - - - -
311A ALA* 1.3 77.4 - - + +
313A MET* 1.3 60.2 + - + +
314A GLU* 3.7 0.9 - - - -
315A PRO* 3.7 10.6 - - - +
316A PHE* 3.8 16.6 - - - -
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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