Contacts of the helix formed by residues 281 - 295 (chain S) in PDB entry 1P9D
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 MET 281 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278S LEU* 2.5 63.2 + - + +
279S SER* 3.8 10.3 - - - +
280S SER* 1.3 74.4 - - - +
282S THR* 1.3 57.4 + - - +
283S GLU* 2.4 22.0 + - - +
284S GLU* 2.7 26.3 + - + +
285S GLU* 3.0 48.3 + - + +
289S TYR* 4.8 4.9 - - + +
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Residues in contact with THR 282 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277S ASP 4.7 2.9 - - - +
278S LEU* 2.9 21.1 - - - +
280S SER* 4.0 10.5 - - - +
281S MET* 1.3 80.9 - - - +
283S GLU* 1.3 63.4 + - + +
286S GLN* 2.6 62.6 + - - +
39U ASP 4.1 9.5 + - - +
40U ALA* 4.7 3.6 - - - -
77U THR* 3.4 1.4 - - - -
78U LYS* 3.2 35.8 + - + +
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Residues in contact with GLU 283 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281S MET 2.4 9.3 + - - +
282S THR* 1.3 80.9 + - + +
284S GLU* 1.3 54.2 + - + +
287S ILE* 2.5 50.5 + - + +
76U VAL 3.8 0.4 - - - -
77U THR* 2.8 44.3 + - + +
78U LYS 4.4 7.1 - - - +
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Residues in contact with GLU 284 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281S MET* 2.7 24.5 + - + +
283S GLU* 1.3 81.3 - - + +
285S GLU* 1.3 74.4 + - - +
287S ILE* 3.0 13.1 - - + +
288S ALA* 2.7 38.1 + - - +
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Residues in contact with GLU 285 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278S LEU* 3.3 14.8 - - + -
281S MET* 3.0 56.6 + - + +
284S GLU* 1.3 109.8 - - - +
286S GLN* 1.3 52.8 + - - +
287S ILE 3.4 0.2 - - - -
288S ALA* 4.3 4.5 - - - +
289S TYR* 2.5 80.0 + - + +
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Residues in contact with GLN 286 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276S PRO* 6.1 0.3 - - - +
278S LEU* 3.5 25.0 - - + +
282S THR* 2.6 46.8 + - - +
283S GLU 3.8 0.2 - - - -
285S GLU* 1.3 72.5 - - - +
287S ILE* 1.3 53.7 + - - +
288S ALA 3.4 0.2 - - - -
290S ALA* 2.4 37.3 + - - +
10U LEU* 3.0 24.7 - - + +
40U ALA* 2.3 35.7 + - - +
41U PHE* 3.0 18.0 - - - -
75U MET* 3.5 2.8 - - - +
76U VAL 2.6 34.9 + - - +
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Residues in contact with ILE 287 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283S GLU* 2.5 48.8 + - + +
284S GLU* 3.0 23.6 - - + +
286S GLN* 1.3 77.8 - - - +
288S ALA* 1.3 85.7 + - + +
290S ALA 3.9 0.2 - - - -
291S MET* 3.1 45.5 + - + +
75U MET* 3.9 27.6 - - + -
76U VAL 4.9 2.7 - - - +
77U THR* 5.0 5.8 - - + -
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Residues in contact with ALA 288 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284S GLU 2.7 19.1 - - - +
285S GLU* 4.3 9.0 - - - +
287S ILE* 1.3 89.3 - - + +
289S TYR* 1.3 70.5 + - + +
291S MET* 4.0 2.3 - - - +
292S GLN* 3.2 25.6 + - - +
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Residues in contact with TYR 289 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278S LEU* 3.5 17.7 - - + -
281S MET* 4.8 4.6 - - + +
285S GLU* 2.5 61.6 + - + +
288S ALA* 1.3 82.4 - - + +
290S ALA* 1.3 56.2 + - - +
292S GLN* 3.4 13.3 + - - +
293S MET* 2.6 37.8 + - - +
10U LEU* 2.8 37.7 - - + +
11U GLN* 4.6 6.7 - - + -
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Residues in contact with ALA 290 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286S GLN 2.4 31.9 + - - +
288S ALA 3.3 0.2 - - - -
289S TYR* 1.3 78.5 - - - +
291S MET* 1.3 51.3 + - - +
294S SER* 2.6 38.2 + - - -
10U LEU* 3.6 6.8 - - + +
73U VAL* 3.0 30.4 - - + +
75U MET* 3.1 26.5 - - + -
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Residues in contact with MET 291 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287S ILE* 3.1 27.7 + - + +
288S ALA* 4.0 3.4 - - - +
290S ALA* 1.3 79.7 - - - +
292S GLN* 1.3 64.6 + - - +
294S SER* 2.4 27.7 + - - +
295S LEU* 3.2 15.5 + - + +
49U ILE* 5.4 2.9 - - + -
54U ILE* 4.8 10.8 - - + -
75U MET* 3.3 33.0 - - + -
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Residues in contact with GLN 292 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288S ALA 3.2 17.1 + - - +
289S TYR* 3.6 15.2 - - - +
291S MET* 1.3 78.3 - - - +
293S MET* 1.3 60.7 + - + +
295S LEU* 4.2 12.3 + - - +
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Residues in contact with MET 293 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289S TYR* 2.6 25.8 - - - +
292S GLN* 1.3 77.3 - - + +
294S SER* 1.3 63.6 + - - +
295S LEU 3.1 2.7 - - - -
296S GLN* 3.1 21.4 + - - +
8U LYS* 3.5 54.2 - - + +
9U THR 3.0 11.9 - - - +
10U LEU* 2.7 54.1 - - - +
12U GLN* 3.6 7.9 - - - +
71U PHE* 4.1 1.6 - - - -
73U VAL* 3.3 12.5 - - + +
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Residues in contact with SER 294 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290S ALA 2.6 20.7 + - - -
291S MET* 2.4 31.9 + - - +
293S MET* 1.3 73.0 - - - +
295S LEU* 1.3 63.1 + - - +
296S GLN* 3.0 10.7 + - - +
49U ILE* 3.2 47.4 - - - +
51U ALA* 4.3 5.5 + - - -
52U GLY* 4.3 11.2 + - - -
71U PHE 5.3 1.9 - - - +
73U VAL* 3.6 9.6 - - - +
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Residues in contact with LEU 295 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291S MET* 3.2 15.6 + - + +
292S GLN* 4.5 8.7 - - - +
293S MET 3.1 1.9 - - - -
294S SER* 1.3 83.6 + - - +
296S GLN* 1.3 51.7 + - - -
297S GLY* 2.4 24.6 + - - -
298S ALA* 3.8 34.0 + - + +
299S GLU* 5.1 13.9 - - + +
301S GLY 4.9 4.7 - - - +
51U ALA 5.5 0.2 - - - +
52U GLY* 4.7 15.0 - - - -
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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