Contacts of the helix formed by residues 233 - 238 (chain D) in PDB entry 1P7L
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 GLY 233 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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885C SAM 5.1 1.3 - - - -
82D MET 4.3 5.0 - - - +
83D GLY* 5.0 2.1 - - - -
163D ASP* 3.6 8.7 - - - -
188D GLN* 2.9 28.1 + - - +
230D PHE* 3.7 4.3 - - - -
232D ILE* 1.3 76.0 - - - +
234D GLY* 1.3 70.5 + - - +
236D MET* 3.5 10.2 + - - +
237D GLY* 3.4 12.1 + - - -
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Residues in contact with GLY 234 (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 PRO* 3.8 13.2 - - - +
77D TYR* 3.1 24.4 + - - -
163D ASP* 2.8 18.3 + - - -
233D GLY* 1.3 75.8 - - - +
235D PRO* 1.3 64.9 - - - +
236D MET 2.7 12.5 + - - -
237D GLY 2.8 9.0 + - - -
238D ASP* 3.1 8.8 + - - +
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Residues in contact with PRO 235 (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 PRO* 4.0 3.6 - - + -
18D ILE* 4.1 20.4 - - + -
45D VAL* 3.6 22.0 - - + +
46D LYS* 3.1 57.9 - - - +
47D THR 3.4 2.9 + - - -
77D TYR* 4.7 1.8 - - + -
84D PHE* 3.4 33.4 - - + -
234D GLY* 1.3 81.1 - - - +
236D MET* 1.3 61.3 + - - +
237D GLY 3.4 0.2 - - - -
238D ASP 3.2 16.6 + - - +
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Residues in contact with MET 236 (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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87A ASN* 3.7 25.6 - - + +
88A SER* 4.0 11.2 - - - -
55C GLU* 4.6 0.5 - - - +
97C LYS 5.0 6.9 - - - +
99C SER* 5.4 0.9 + - - -
46D LYS* 3.5 13.5 + - - -
47D THR* 3.9 24.0 + - + +
80D SER 5.6 0.4 - - - +
83D GLY* 3.6 36.9 + - - +
232D ILE* 3.9 25.1 - - + +
233D GLY 3.6 10.1 - - - +
234D GLY 2.7 6.3 + - - -
235D PRO* 1.3 76.3 - - - +
237D GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 237 (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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55C GLU* 4.0 12.3 - - - +
99C SER* 4.4 13.7 + - - -
102C ILE* 4.1 14.9 - - - +
885C SAM 4.1 9.0 + - - -
232D ILE* 4.1 17.3 - - - -
233D GLY* 3.4 9.5 + - - -
234D GLY 2.8 6.7 + - - -
236D MET* 1.3 81.2 - - - +
238D ASP* 1.3 64.7 + - - +
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Residues in contact with ASP 238 (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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55C GLU* 3.2 4.5 - - - +
885C SAM 2.9 75.0 + - - +
14D HIS* 4.3 1.7 + - - -
15D PRO* 3.1 21.7 - - + +
163D ASP* 5.6 0.2 - - - +
234D GLY 3.1 3.8 + - - +
235D PRO* 3.2 14.9 + - - +
236D MET 3.4 1.4 - - - -
237D GLY* 1.3 80.8 - - - +
239D CYS* 1.3 67.2 + - - +
884D PPK 3.8 15.4 + - - +
886D K 3.1 16.4 - - - -
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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