Contacts of the helix formed by residues 300 - 314 (chain A) in PDB entry 4DVQ
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 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LYS* 3.7 18.0 + - - -
139A PHE* 5.8 0.8 - - - -
298A GLU 4.1 0.6 + - - -
299A LEU* 1.3 77.5 - - - +
301A LEU* 1.3 53.8 + - - +
302A GLU* 3.2 7.4 + - - +
303A ALA* 3.0 27.3 + - - +
304A ILE* 2.8 32.3 + - - +
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Residues in contact with LEU 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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271A ILE* 6.0 2.7 - - + -
275A TYR* 3.9 36.8 - - + +
294A LEU* 3.7 28.3 - - + -
299A LEU 3.7 1.0 + - - -
300A SER* 1.3 73.8 - - - +
302A GLU* 1.3 61.2 + - + +
304A ILE* 3.3 8.7 + - + +
305A LYS* 2.8 64.7 + - + +
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Residues in contact with GLU 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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124A GLY 4.6 7.9 - - - +
125A HIS* 4.5 13.9 + - - -
126A LYS* 4.0 29.7 + - + +
300A SER* 3.2 8.1 + - - +
301A LEU* 1.3 81.8 - - + +
303A ALA* 1.3 56.2 + - - +
305A LYS* 3.6 32.2 + - - +
306A ALA* 3.0 27.0 + - - +
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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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126A LYS* 4.3 14.3 - - + +
127A CYS 6.0 0.2 - - - -
140A ASN* 4.0 18.2 - - - +
299A LEU* 3.9 19.1 - - + -
300A SER* 3.0 22.5 + - - +
302A GLU* 1.3 76.2 - - - +
304A ILE* 1.3 65.3 + - - +
306A ALA* 3.1 5.8 + - - +
307A ASN* 2.9 31.2 + - - +
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Residues in contact with ILE 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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271A ILE* 4.9 4.9 - - + -
290A VAL* 4.5 10.5 - - + -
293A LEU* 3.9 43.0 - - + +
294A LEU* 3.7 40.6 - - + -
297A ALA* 4.9 3.8 - - + -
299A LEU* 3.5 37.0 - - + +
300A SER 2.8 18.7 + - - +
301A LEU* 3.7 8.5 - - + +
303A ALA* 1.3 72.1 - - - +
305A LYS* 1.3 59.1 + - - +
307A ASN* 3.8 4.7 - - - +
308A SER* 2.8 28.6 + - - -
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Residues in contact with LYS 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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268A ASP* 4.7 10.9 + - - +
271A ILE* 4.2 36.2 - - + +
275A TYR* 6.5 0.4 - - - -
301A LEU* 2.8 49.1 + - + +
302A GLU* 3.6 33.2 + - - +
304A ILE* 1.3 74.1 - - - +
306A ALA* 1.3 62.2 + - - +
308A SER* 3.2 6.2 + - - -
309A MET* 3.0 28.5 + - + +
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Residues in contact with ALA 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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120A ARG* 5.8 0.5 + - - -
125A HIS* 5.9 1.1 - - + -
126A LYS* 3.4 32.3 - - + +
127A CYS 3.9 2.2 - - - +
128A GLY* 3.7 16.8 + - - +
264A PHE* 6.2 3.1 - - - -
302A GLU 3.0 18.5 + - - +
303A ALA* 3.1 5.8 + - - +
305A LYS* 1.3 76.8 - - - +
307A ASN* 1.3 60.5 + - - +
309A MET* 3.6 6.7 + - - +
310A GLU* 3.4 23.4 + - - +
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Residues in contact with ASN 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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127A CYS 5.2 0.2 + - - -
128A GLY* 3.9 6.8 - - - -
129A VAL* 2.9 30.1 + - - +
140A ASN* 2.9 25.5 + - - +
144A LEU* 3.4 37.0 - - + +
293A LEU* 5.5 1.3 - - + -
299A LEU* 4.1 5.5 - - - +
303A ALA* 2.9 28.5 + - - +
304A ILE* 4.1 3.4 - - - +
306A ALA* 1.3 72.1 - - - +
308A SER* 1.3 66.2 + - - +
309A MET 3.1 1.6 - - - -
310A GLU* 3.1 6.6 + - + +
311A LEU* 3.1 31.1 + - + +
451A LEU* 5.6 1.1 - - + +
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Residues in contact with SER 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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204A LEU* 5.2 0.3 - - - +
205A PHE* 3.3 30.8 - - - -
267A GLY 5.1 0.9 + - - -
271A ILE* 3.7 20.1 - - - +
290A VAL* 3.9 14.0 - - - +
293A LEU* 5.8 1.5 - - - +
304A ILE* 2.8 24.7 + - - -
305A LYS 3.7 3.4 - - - -
307A ASN* 1.3 72.6 - - - +
309A MET* 1.3 58.5 + - - +
311A LEU* 3.4 10.4 + - - +
312A THR* 2.9 33.1 + - - -
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Residues in contact with MET 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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120A ARG* 5.6 3.6 - - - +
260A TRP* 4.6 2.2 - - + -
263A ILE* 3.6 45.3 - - + +
264A PHE* 3.7 48.0 - - + +
267A GLY* 3.6 26.7 - - - +
268A ASP* 4.9 1.1 - - + +
271A ILE* 6.4 0.9 - - + -
305A LYS 3.0 18.1 + - - +
306A ALA* 3.7 7.0 - - - +
307A ASN 3.1 0.2 - - - -
308A SER* 1.3 79.6 - - - +
310A GLU* 1.3 56.4 + - - +
312A THR* 3.9 3.8 - - - -
313A ALA* 2.9 30.7 + - + +
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Residues in contact with GLU 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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116A TRP* 6.6 0.2 - - - -
120A ARG* 4.6 10.7 + - - +
128A GLY* 3.1 33.9 + - - +
129A VAL* 3.3 4.4 + - - +
130A PHE* 2.8 37.4 + - - +
131A LEU* 3.9 17.7 - - - +
306A ALA 3.4 12.7 + - - +
307A ASN* 3.1 9.1 + - - +
309A MET* 1.3 73.9 - - - +
311A LEU* 1.3 57.9 + - + +
314A GLY* 2.8 32.1 + - - -
601A HEM 3.9 12.8 - - + +
602A 1CA 3.3 29.7 - - + +
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Residues in contact with LEU 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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144A LEU* 5.4 1.3 - - + -
148A VAL* 4.1 36.3 - - + -
204A LEU* 3.8 30.6 - - + +
289A ILE* 4.7 4.5 - - + -
290A VAL* 5.3 1.6 - - + -
293A LEU* 5.1 8.3 - - + -
307A ASN* 3.1 23.4 + - + +
308A SER* 3.7 8.7 - - - +
310A GLU* 1.3 76.6 - - + +
312A THR* 1.3 57.1 + - - +
315A SER* 2.9 32.7 + - - -
451A LEU* 4.2 17.3 - - + -
601A HEM 3.6 35.2 - - + +
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Residues in contact with THR 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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201A ASN* 5.6 1.6 - - - +
204A LEU* 4.1 5.2 - - + +
205A PHE* 3.4 31.3 - - + -
223A PHE* 3.7 13.3 - - + -
263A ILE 6.0 0.2 - - - +
266A TYR* 3.8 33.9 - - + -
267A GLY* 4.5 12.2 + - - -
270A CYS* 5.2 0.4 - - - -
308A SER 2.9 18.6 + - - -
309A MET* 3.9 7.9 - - + -
311A LEU* 1.3 72.3 - - - +
313A ALA* 1.3 69.0 + - - +
315A SER* 3.2 14.8 + - - +
316A VAL* 3.9 4.7 - - - +
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Residues in contact with ALA 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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223A PHE* 4.4 5.8 - - - -
227A LEU* 3.6 31.7 - - + +
230A MET* 5.4 0.7 - - + -
231A PHE* 5.5 0.9 - - - -
260A TRP* 4.5 9.6 - - + -
263A ILE* 4.0 23.1 - - + -
309A MET* 2.9 21.2 + - + +
312A THR* 1.3 79.2 - - - +
314A GLY* 1.3 59.7 + - - +
315A SER 3.3 4.0 + - - -
316A VAL* 4.3 4.5 + - - +
317A ASP* 4.9 1.7 + - - +
602A 1CA 4.1 18.1 - - + +
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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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310A GLU 2.8 22.1 + - - -
311A LEU 3.9 1.1 - - - -
312A THR 3.3 0.2 - - - -
313A ALA* 1.3 73.2 - - - +
315A SER* 1.3 53.0 + - - +
316A VAL 3.5 1.8 - - - -
317A ASP 5.3 0.4 - - - -
318A THR* 2.7 30.7 + - - +
601A HEM 3.4 14.4 - - - -
602A 1CA 3.5 30.1 - - - +
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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