Contacts of the helix formed by residues 249 - 260 (chain A) in PDB entry 3P3W
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 ASN 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ASN* 3.4 27.5 + - + +
247A ASN 3.2 0.4 - - - -
248A GLU* 1.3 76.1 - - - +
250A PRO* 1.4 72.3 - - - +
251A MET* 2.9 36.7 + - - +
252A VAL* 3.1 26.0 + - + +
253A GLN* 3.1 13.7 + - - +
336A GLN* 5.5 4.0 + - - -
337A GLY 4.2 15.5 + - - -
338A MET 4.7 4.0 + - - +
340A GLY* 5.7 3.4 - - - +
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Residues in contact with PRO 250 (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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248A GLU 3.3 9.1 - - - +
249A ASN* 1.4 89.1 - - - +
251A MET* 1.3 57.6 + - + +
253A GLN* 3.8 11.8 - - + +
254A GLN* 2.9 31.3 + - - +
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Residues in contact with MET 251 (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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249A ASN* 2.9 14.1 + - - +
250A PRO* 1.3 78.3 - - + +
252A VAL* 1.3 62.8 + - + +
254A GLN* 3.3 22.1 + - - +
255A PHE* 2.9 28.2 + - + +
283A HIS* 6.3 1.8 - - + -
287A LEU* 5.7 4.5 - - - -
336A GLN* 3.4 29.4 - - + +
337A GLY* 4.3 15.0 - - - +
338A MET* 4.9 6.5 - - + -
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Residues in contact with VAL 252 (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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245A VAL* 4.4 11.4 - - + -
246A ASN 3.6 22.4 - - - +
247A ASN* 4.7 11.0 - - - +
249A ASN* 3.1 19.4 + - + +
251A MET* 1.3 76.5 - - - +
253A GLN* 1.3 52.8 - - + +
255A PHE* 3.0 7.4 + - - +
256A ILE* 2.8 50.5 + - + +
338A MET* 3.8 53.2 - - + +
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Residues in contact with GLN 253 (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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247A ASN 2.7 29.2 + - - +
248A GLU* 3.6 19.8 + - - +
249A ASN 3.1 10.4 + - - +
250A PRO* 4.0 8.6 - - + +
252A VAL* 1.3 75.9 - - + +
254A GLN* 1.3 60.4 + - - +
256A ILE* 4.1 7.1 - - - +
257A GLN* 3.2 33.1 + - + +
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Residues in contact with GLN 254 (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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250A PRO 2.9 23.2 + - - +
251A MET* 3.3 21.7 + - - +
253A GLN* 1.3 77.7 - - - +
255A PHE* 1.3 59.0 + - - +
257A GLN* 4.0 12.0 + - - +
258A ARG* 2.9 41.4 + - - +
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Residues in contact with PHE 255 (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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22A ALA* 6.0 2.2 - - + -
25A PHE* 3.7 30.2 - + - -
29A LEU* 4.6 4.3 - - + -
251A MET* 2.9 14.0 + - + +
252A VAL* 3.0 8.3 + - - +
254A GLN* 1.3 76.9 - - - +
256A ILE* 1.3 70.9 + - + +
258A ARG* 3.2 12.1 + - - +
259A TRP* 3.0 62.3 + + + +
275A LEU* 5.1 7.6 - - + -
279A SER 6.1 0.2 - - - -
280A ALA* 6.3 0.7 - - - -
283A HIS* 4.1 31.6 - + + -
338A MET* 3.7 38.8 - - + -
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Residues in contact with ILE 256 (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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252A VAL* 2.8 36.1 + - + +
253A GLN* 4.2 7.6 - - - +
254A GLN 3.5 0.2 - - - -
255A PHE* 1.3 87.5 - - + +
257A GLN* 1.3 64.6 + - - +
258A ARG 3.1 2.5 - - - -
259A TRP* 2.9 31.7 + - + +
260A VAL* 3.2 28.8 + - + +
275A LEU* 5.0 15.5 - - + -
338A MET* 5.2 0.9 - - + -
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Residues in contact with GLN 257 (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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253A GLN* 3.2 19.9 + - + +
254A GLN* 4.1 9.0 - - - +
255A PHE 3.3 0.4 - - - -
256A ILE* 1.3 80.5 - - - +
258A ARG* 1.3 61.3 + - + +
260A VAL* 4.0 13.5 - - - +
261A ARG* 4.7 5.7 - - - +
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Residues in contact with ARG 258 (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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25A PHE* 4.0 23.7 - - + -
29A LEU* 6.5 1.6 - - - -
254A GLN* 2.9 46.5 + - - +
255A PHE* 3.2 10.7 + - - +
256A ILE 3.1 0.4 - - - -
257A GLN* 1.3 79.8 - - + +
259A TRP* 1.3 65.4 + - - +
260A VAL 3.4 0.7 - - - -
261A ARG* 3.3 16.9 + - - +
262A LEU* 3.3 15.7 - - - +
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Residues in contact with TRP 259 (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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18A GLN* 4.2 25.2 - - + +
21A SER* 3.9 16.4 - - - -
22A ALA* 3.7 40.6 - - + -
25A PHE* 4.2 13.2 - + + -
255A PHE* 3.0 44.8 + + + +
256A ILE* 2.9 27.0 + - + +
258A ARG* 1.3 78.3 - - - +
260A VAL* 1.3 68.1 + - + +
262A LEU* 3.3 32.5 + - + +
267A PHE* 5.8 0.7 - + - -
270A ALA* 3.7 38.2 + - + +
273A ALA 5.2 1.0 + - - -
275A LEU* 4.9 19.4 - - + +
279A SER* 5.5 0.2 - - - -
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Residues in contact with VAL 260 (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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256A ILE* 3.2 28.4 + - + +
257A GLN* 4.0 12.1 - - - +
259A TRP* 1.3 83.7 - - + +
261A ARG* 1.3 64.8 + - + +
262A LEU 3.3 4.3 + - - +
270A ALA 4.7 8.3 - - - +
271A LYS* 4.9 13.1 + - - +
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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