Contacts of the helix formed by residues 238 - 244 (chain A) in PDB entry 3AP1
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 TYR 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A A3P 2.7 47.1 + + - -
79A SER 3.4 17.5 - - - +
80A GLY* 3.7 19.5 - - - -
83A LEU* 4.3 6.5 - - + -
181A MET* 4.0 12.3 - - + -
182A VAL 2.8 16.1 + - - +
183A ARG* 3.4 42.6 - - + -
236A VAL 3.4 2.8 + - - -
237A TYR* 1.3 70.3 - - - +
239A GLU* 1.3 64.7 + - + +
241A LEU* 3.2 5.3 + - + +
242A VAL* 3.0 46.7 + - + +
294A ASN 4.9 0.5 + - - -
297A ALA* 3.6 17.8 - - - +
298A LEU* 4.0 19.9 + - + +
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Residues in contact with GLU 239 (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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182A VAL 4.0 2.4 - - - +
183A ARG* 3.3 15.4 + - - +
184A ASP* 3.0 30.0 + - - +
187A ALA* 5.0 1.0 - - - +
237A TYR* 4.5 3.6 - - - +
238A TYR* 1.3 78.6 + - + +
240A GLN* 1.3 64.5 + - - +
242A VAL* 3.6 1.4 + - - +
243A LEU* 2.9 35.2 + - - +
298A LEU* 3.8 25.4 - - + +
325A TYR* 2.6 32.9 + - - -
334A TYR* 3.7 40.2 - - + -
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Residues in contact with GLN 240 (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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237A TYR* 3.1 28.5 + - + +
239A GLU* 1.3 85.6 - - + +
241A LEU* 1.3 58.0 + - - +
243A LEU* 4.4 1.7 - - - +
244A HIS* 2.8 55.1 + - + +
248A SER* 3.1 14.5 + - - +
334A TYR* 3.1 26.5 + - - +
335A GLY* 5.7 0.4 - - - -
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Residues in contact with LEU 241 (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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80A GLY 4.8 0.2 - - - +
83A LEU* 3.9 31.2 - - + -
84A MET* 4.3 13.2 - - - +
87A MET* 3.7 16.6 - - + -
181A MET* 4.0 21.8 - - + -
236A VAL* 4.4 12.6 - - + -
237A TYR 2.9 13.6 + - - +
238A TYR* 3.3 12.1 - - + +
240A GLN* 1.3 76.6 - - - +
242A VAL* 1.3 56.4 + - - +
245A PRO* 3.1 35.9 - - + +
248A SER* 3.4 14.7 + - - -
249A LEU* 3.4 33.2 - - + -
293A VAL* 4.3 0.8 - - + +
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Residues in contact with VAL 242 (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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1A A3P 3.9 10.1 - - + -
83A LEU* 4.3 7.2 - - + -
238A TYR* 3.0 54.4 + - + +
239A GLU 3.9 3.6 - - - +
241A LEU* 1.3 78.0 - - - +
243A LEU* 1.3 64.9 + - - +
244A HIS 3.5 0.2 + - - -
245A PRO* 3.5 0.7 - - - +
293A VAL* 3.7 8.4 - - + +
294A ASN 3.3 27.8 - - - +
295A LEU* 4.0 11.2 - - + -
298A LEU* 3.9 18.4 - - + -
341A VAL* 3.2 23.4 - - - +
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Residues in contact with LEU 243 (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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239A GLU 2.9 22.2 + - - +
240A GLN* 4.2 7.0 - - - +
242A VAL* 1.3 75.7 - - - +
244A HIS* 1.3 75.3 + - + +
245A PRO* 3.6 0.7 - - - -
295A LEU* 3.7 11.7 - - + -
298A LEU* 3.6 24.5 - - + -
334A TYR* 3.4 41.7 - - + +
335A GLY* 3.7 14.8 - - - +
336A ASN 3.9 3.6 - - - +
337A PRO* 3.6 26.6 - - + +
338A ASP* 3.0 31.9 + - - +
341A VAL* 3.6 2.9 - - - +
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Residues in contact with HIS 244 (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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240A GLN* 2.8 42.5 + - + +
243A LEU* 1.3 87.1 + - + +
245A PRO* 1.3 61.3 - - - +
246A ARG 3.3 2.6 + - - -
247A ARG* 3.6 14.7 + - + -
248A SER* 2.8 28.9 + - - +
335A GLY* 5.4 1.2 - - - -
336A ASN 2.9 32.1 + - - -
337A PRO 4.8 0.2 - - - -
338A ASP* 2.7 31.2 + - - +
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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