Contacts of the helix formed by residues 300 - 313 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A HIS* 6.6 0.4 - - + -
77A ARG* 4.7 14.1 - - - +
120A LEU* 3.8 10.5 - - + -
127A ALA* 3.7 31.0 - - + -
131A LEU* 5.2 2.9 - - + -
268A SER* 5.4 1.3 - - - +
298A TYR 4.4 0.4 - - - +
299A MET* 1.3 87.0 - - + +
301A PRO* 1.3 76.3 - - + +
302A ALA* 4.5 3.1 - - + +
303A HIS* 2.8 48.6 + - + +
304A ARG 2.8 10.6 + - - -
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Residues in contact with PRO 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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118A LEU* 3.3 26.5 - - - +
119A GLU* 3.8 26.2 - - + +
120A LEU* 4.7 1.3 - - + -
299A MET 3.4 0.4 - - - +
300A PRO* 1.3 86.0 - - + +
302A ALA* 1.3 59.8 + - + +
304A ARG* 3.1 34.6 + - - +
305A ASN* 2.8 38.9 + - - +
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Residues in contact with ALA 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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14A ALA 5.0 2.5 - - - +
15A TYR* 3.7 29.2 - - - +
16A HIS* 3.8 30.7 - - + +
300A PRO* 3.2 3.3 - - + -
301A PRO* 1.3 82.6 - - + +
303A HIS* 1.3 60.3 + - + +
305A ASN* 3.4 12.4 + - - +
306A PHE* 3.1 21.3 + - - +
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Residues in contact with HIS 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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15A TYR 3.3 17.9 - - - -
16A HIS* 3.0 25.8 + - - +
17A ILE* 4.0 2.0 - - + +
23A PHE* 3.2 59.3 - + + +
77A ARG* 5.9 3.8 - - - -
131A LEU* 4.8 3.6 - - + +
268A SER* 4.1 11.6 + - - +
299A MET* 4.7 2.0 - - + -
300A PRO* 2.8 40.0 + - + +
302A ALA* 1.3 77.4 - - + +
304A ARG* 1.3 66.4 + - - +
305A ASN 3.2 0.2 - - - -
306A PHE* 3.2 6.4 + - - +
307A LEU* 3.1 29.5 + - - +
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Residues in contact with ARG 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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119A GLU* 2.8 37.2 + - - +
296A ARG* 3.1 37.2 + - + +
297A ARG* 3.2 24.2 + - - +
299A MET* 2.5 37.2 + - + +
300A PRO 2.8 5.9 + - - -
301A PRO* 3.3 32.4 - - - +
303A HIS* 1.3 78.3 - - - +
305A ASN* 1.3 64.9 + - - +
307A LEU* 3.4 9.1 + - - +
308A CYS* 3.2 25.7 + - - -
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Residues in contact with ASN 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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15A TYR* 4.0 14.7 - - + -
301A PRO* 2.8 28.1 + - - +
302A ALA* 3.6 9.9 - - - +
304A ARG* 1.3 78.3 - - - +
306A PHE* 1.3 64.0 + - - +
308A CYS* 3.1 7.3 + - - +
309A SER* 2.9 24.1 + - - -
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Residues in contact with PHE 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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12A SER* 5.2 8.3 - - - -
15A TYR* 3.5 42.3 - + + +
17A ILE* 4.3 13.0 - - + -
23A PHE* 4.1 21.3 - + - -
178A ILE* 4.6 11.4 - - + -
181A ILE* 4.4 16.4 - - + -
182A PRO* 6.5 0.9 - - + -
272A CYS* 3.9 16.2 - - - -
302A ALA 3.1 14.0 + - - +
303A HIS* 3.2 11.2 + - - +
305A ASN* 1.3 76.3 - - - +
307A LEU* 1.3 68.6 + - + +
309A SER* 3.1 6.9 + - - -
310A LEU* 3.1 59.2 + - + +
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Residues in contact with LEU 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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23A PHE* 5.2 0.7 - - + -
268A SER* 4.4 8.1 - - - +
271A GLN* 4.1 14.1 - - + +
272A CYS* 3.6 38.1 - - + +
275A VAL* 4.2 9.9 - - + +
296A ARG* 3.9 35.0 - - - +
299A MET* 3.9 25.6 - - - -
303A HIS 3.1 14.5 + - - +
304A ARG* 3.7 7.6 - - - +
305A ASN 3.3 0.2 - - - -
306A PHE* 1.3 86.3 - - + +
308A CYS* 1.3 58.5 + - - +
310A LEU* 3.5 5.1 + - - +
311A GLU* 3.1 29.5 + - - +
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Residues in contact with CYS 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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296A ARG* 4.3 16.2 - - - -
304A ARG* 3.2 15.0 + - - +
305A ASN* 3.1 10.2 + - - +
307A LEU* 1.3 77.6 - - - +
309A SER* 1.3 66.8 + - - +
311A GLU* 3.1 13.0 + - - +
312A SER* 3.1 20.8 + - - -
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Residues in contact with SER 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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15A TYR* 3.4 32.0 + - - -
305A ASN 2.9 14.7 + - - -
306A PHE* 3.1 9.5 + - - -
308A CYS* 1.3 76.2 - - - +
310A LEU* 1.3 67.4 + - - +
312A SER* 2.5 32.4 + - - -
313A ASN* 3.1 15.2 + - - +
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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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181A ILE* 4.1 10.8 - - + -
185A PHE* 3.8 30.8 - - + -
272A CYS* 3.9 15.5 - - - +
275A VAL* 3.7 30.4 - - + +
276A LEU* 4.7 8.1 - - + +
306A PHE* 3.1 51.3 + - + +
307A LEU* 3.6 8.7 - - + +
309A SER* 1.3 87.0 + - - +
311A GLU* 1.3 62.3 + - - +
312A SER 3.0 1.0 + - - -
313A ASN* 3.3 23.7 + - - +
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Residues in contact with GLU 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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275A VAL* 4.1 21.4 - - + +
280A GLN* 6.2 1.8 - - - +
282A THR* 4.0 24.1 - - - +
296A ARG* 3.2 28.1 + - - -
307A LEU 3.1 13.1 + - - +
308A CYS* 3.1 16.5 + - - +
310A LEU* 1.3 75.3 - - - +
312A SER* 1.3 57.9 + - - +
313A ASN 4.1 3.7 - - - +
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Residues in contact with SER 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 CYS 3.1 9.7 + - - -
309A SER* 2.5 26.0 + - - -
311A GLU* 1.3 77.0 - - - +
313A ASN* 1.3 71.3 + - - +
314A PRO* 3.9 0.9 - - - +
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Residues in contact with ASN 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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185A PHE* 3.5 47.2 - - + -
309A SER* 3.1 20.3 + - - +
310A LEU* 3.3 16.5 + - - +
311A GLU 4.1 4.2 - - - +
312A SER* 1.3 87.5 + - - +
314A PRO* 1.3 79.5 - - + +
315A SER* 3.6 1.7 + - - -
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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