Contacts of the helix formed by residues 300 - 313 (chain D) in PDB entry 7A62
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 PRO 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D ARG* 5.0 12.8 - - - +
120D LEU* 3.8 10.5 - - + -
127D ALA* 3.7 31.4 - - + -
131D LEU* 5.1 3.4 - - + -
268D SER* 5.2 1.1 - - - +
299D MET* 1.3 87.7 - - + +
301D PRO* 1.3 76.1 - - + +
302D ALA* 4.5 3.1 - - + +
303D HIS* 2.9 49.3 + - + +
304D ARG 3.0 9.9 + - - -
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Residues in contact with PRO 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU 3.4 27.4 - - - +
119D GLU* 3.9 27.8 - - + +
120D LEU* 4.7 2.0 - - + -
299D MET 3.4 0.4 - - - +
300D PRO* 1.3 85.9 - - + +
302D ALA* 1.3 59.3 + - + +
304D ARG* 3.1 32.0 + - - +
305D ASN* 2.9 39.0 + - - +
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Residues in contact with ALA 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ALA 4.9 2.0 - - - +
15D TYR* 3.4 36.6 - - - +
16D HIS* 3.8 22.4 - - + +
300D PRO* 3.2 3.1 - - + -
301D PRO* 1.3 81.6 - - + +
303D HIS* 1.3 60.7 + - + +
305D ASN* 3.5 8.8 + - - +
306D PHE* 3.1 25.1 + - - +
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Residues in contact with HIS 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TYR 3.2 17.7 - - - -
16D HIS* 2.8 25.4 + - - +
17D ILE* 4.3 2.0 - - + -
23D PHE* 3.2 61.2 - + + +
77D ARG* 6.1 2.0 - - - -
131D LEU* 4.8 2.5 - - + +
268D SER* 4.1 12.6 + - - +
299D MET* 4.7 1.3 - - + -
300D PRO* 2.9 39.8 + - + +
302D ALA* 1.3 77.6 - - + +
304D ARG* 1.3 66.4 + - - +
306D PHE* 3.3 7.1 + - - +
307D LEU* 3.0 29.2 + - - +
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Residues in contact with ARG 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D GLU* 2.9 33.1 + - - +
296D ARG* 3.0 38.1 + - + +
297D ARG* 3.5 27.0 + - - +
299D MET* 3.3 17.9 + - + +
300D PRO 3.0 9.1 + - - +
301D PRO* 3.4 31.7 - - - +
303D HIS* 1.3 77.2 - - - +
305D ASN* 1.3 65.5 + - - +
307D LEU* 3.3 9.6 + - - +
308D CYS* 3.0 27.9 + - - -
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Residues in contact with ASN 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TYR* 3.8 15.8 - - + -
301D PRO* 2.9 27.4 + - - +
302D ALA* 3.8 8.6 - - - +
304D ARG* 1.3 74.6 - - - +
306D PHE* 1.3 61.9 + - - +
308D CYS* 2.9 10.2 + - - +
309D SER* 2.7 30.1 + - - -
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Residues in contact with PHE 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D SER* 4.2 15.7 - - - -
15D TYR* 3.4 33.3 - + + -
17D ILE* 3.5 31.2 - - + -
23D PHE* 4.2 12.1 - + - -
178D ILE* 4.6 6.5 - - + -
181D ILE* 4.4 16.8 - - + -
182D PRO* 6.3 0.7 - - + -
272D CYS* 4.0 17.0 - - - -
302D ALA 3.1 15.3 + - - +
303D HIS* 3.6 10.5 - - - +
304D ARG 3.3 0.2 - - - -
305D ASN* 1.3 74.6 - - - +
307D LEU* 1.3 69.1 + - + +
309D SER* 3.0 20.9 + - - -
310D LEU* 3.1 41.2 + - + +
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Residues in contact with LEU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 5.2 0.7 - - + -
268D SER* 4.2 11.4 - - - +
271D GLN* 4.1 9.6 - - + +
272D CYS* 3.7 36.8 - - + +
275D VAL* 4.2 6.6 - - + +
296D ARG* 3.8 35.2 - - - +
299D MET* 3.7 32.1 - - + -
303D HIS 3.0 19.2 + - - +
304D ARG* 3.6 7.6 - - - +
306D PHE* 1.3 83.4 - - + +
308D CYS* 1.3 60.7 + - - +
310D LEU* 3.7 6.7 + - + +
311D GLU* 3.2 26.9 + - - +
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Residues in contact with CYS 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D GLN* 5.6 5.2 - - - -
296D ARG* 4.6 11.7 - - - -
304D ARG* 3.0 17.7 + - - +
305D ASN* 2.9 13.2 + - - +
307D LEU* 1.3 75.2 - - - +
309D SER* 1.3 70.1 + - - +
311D GLU* 3.0 18.4 + - - +
312D SER* 3.2 12.0 + - - -
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Residues in contact with SER 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TYR* 3.7 25.7 + - - -
305D ASN 2.7 18.4 + - - -
306D PHE* 3.0 13.0 + - - -
308D CYS* 1.3 71.2 - - - +
310D LEU* 1.3 66.7 + - - +
312D SER* 2.5 33.2 + - - -
313D ASN* 2.5 23.1 + - - +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D ILE* 4.1 19.3 - - + -
185D PHE* 3.4 35.6 - - + -
272D CYS* 4.0 23.3 - - - +
275D VAL* 3.4 20.6 - - + +
276D LEU* 4.7 6.7 - - + +
306D PHE* 3.1 44.2 + - + +
307D LEU* 4.0 3.8 - - + +
309D SER* 1.3 88.1 + - - +
311D GLU* 1.3 63.3 + - - +
312D SER 3.0 1.2 + - - -
313D ASN* 3.3 20.4 + - - +
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Residues in contact with GLU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D VAL* 3.4 17.0 - - + +
282D THR* 3.4 26.5 - - - +
293D GLN* 4.6 3.0 - - - +
296D ARG* 2.9 35.9 + - - -
307D LEU 3.2 8.7 + - - +
308D CYS* 3.0 16.8 + - - +
309D SER 3.0 0.2 + - - -
310D LEU* 1.3 78.6 - - - +
312D SER* 1.3 57.9 + - - +
313D ASN 4.4 3.2 - - - +
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Residues in contact with SER 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D CYS 3.2 7.5 + - - -
309D SER* 2.5 31.1 + - - -
311D GLU* 1.3 72.1 - - - +
313D ASN* 1.3 67.5 + - - +
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Residues in contact with ASN 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D PHE* 3.7 35.8 - - + +
309D SER* 2.5 38.9 + - - +
310D LEU* 3.3 15.0 + - - +
311D GLU 4.4 2.8 - - - +
312D SER* 1.3 82.8 + - - +
314D PRO* 1.3 79.6 - - + +
315D SER* 3.6 0.9 + - - -
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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