Contacts of the helix formed by residues 253 - 267 (chain D) in PDB entry 3EGC
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 SER 253 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D ASN* 5.8 2.7 + - - -
202D ARG* 4.6 4.0 - - - -
251D THR 3.4 1.2 - - - -
252D SER* 1.3 83.1 + - - +
254D HIS* 1.3 62.6 + - - +
255D ARG* 3.5 13.3 + - - +
256D ILE* 3.1 18.8 + - - +
257D THR* 2.8 31.4 + - - -
280D PHE 3.6 9.4 - - - -
281D ASP* 3.2 15.7 - - - -
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Residues in contact with HIS 254 (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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79D ASN* 2.7 33.3 + - - -
80D VAL* 4.2 18.9 - - + +
81D PHE* 5.1 2.9 - - + -
253D SER* 1.3 75.8 - - - +
255D ARG* 1.3 88.8 + - - +
257D THR* 3.2 3.1 + - - -
258D GLU* 2.9 40.7 + - - +
280D PHE 3.3 2.2 + - - -
281D ASP* 3.0 33.9 + - + -
283D LEU* 3.6 33.6 - - + +
285D TRP* 4.5 4.0 + - + -
286D MET* 3.7 22.9 - - + -
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Residues in contact with ARG 255 (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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80C VAL* 5.4 3.8 - - - +
76D ASP* 3.8 20.6 + - - -
78D GLU* 3.8 19.2 + - - +
79D ASN* 3.9 25.1 - - - +
80D VAL* 4.6 1.0 - - - +
231D ASN* 2.7 43.7 + - - +
253D SER* 3.2 7.7 + - - +
254D HIS* 1.3 110.4 - - + +
256D ILE* 1.3 61.1 + - + +
258D GLU* 3.4 21.6 + - - +
259D GLY 3.3 7.4 + - - -
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Residues in contact with ILE 256 (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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190D ILE* 3.4 37.5 - - + +
191D VAL 3.4 3.8 - - - +
192D GLY* 3.3 27.8 - - - +
231D ASN* 3.1 21.4 - - - +
232D GLY* 5.0 1.0 - - - +
251D THR* 3.9 10.1 - - + -
252D SER* 3.0 26.9 - - - +
253D SER* 3.1 19.3 + - - +
255D ARG* 1.3 76.9 - - + +
257D THR* 1.3 66.1 + - - +
259D GLY 3.1 1.2 + - - -
260D ALA* 3.0 21.5 + - - +
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Residues in contact with THR 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D THR* 2.6 26.3 + - - -
253D SER 2.8 9.5 + - - -
254D HIS* 3.5 9.6 - - - -
256D ILE* 1.3 77.3 - - - +
258D GLU* 1.3 56.7 + - - +
260D ALA* 3.3 1.7 + - - +
261D MET* 2.9 32.2 + - + +
277D ILE* 4.0 13.5 - - + -
279D SER* 2.7 22.8 + - - -
285D TRP* 4.2 12.8 - - + -
286D MET* 4.4 3.4 - - + -
293D LEU* 3.8 28.5 - - + -
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Residues in contact with GLU 258 (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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284C PRO* 3.7 33.0 - - + +
285C TRP* 4.9 3.2 + - - +
288C PHE* 3.5 26.8 - - + -
231D ASN* 4.2 5.2 + - - +
254D HIS* 2.9 30.0 + - - +
255D ARG* 3.5 34.4 + - - +
256D ILE 3.2 0.2 - - - -
257D THR* 1.3 76.7 - - - +
259D GLY* 1.3 57.7 + - - +
261D MET 3.2 1.2 + - - -
262D GLN* 2.9 37.2 + - - +
285D TRP* 4.2 19.4 + - + -
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Residues in contact with GLY 259 (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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231D ASN* 3.6 18.1 + - - -
233D ARG* 3.4 19.8 - - - +
255D ARG 3.3 4.9 + - - -
256D ILE 3.1 6.8 + - - -
258D GLU* 1.3 78.9 - - - +
260D ALA* 1.3 51.4 + - - +
262D GLN* 3.1 19.6 + - - +
263D ALA* 2.7 30.1 + - - +
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Residues in contact with ALA 260 (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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190D ILE* 5.2 1.8 - - + -
232D GLY 4.6 1.0 + - - -
236D ALA* 3.9 21.9 - - + +
240D LEU* 5.1 1.1 - - + +
249D LEU* 5.0 8.3 - - + -
251D THR* 3.9 21.3 - - + -
256D ILE* 3.0 16.1 + - + +
257D THR 3.7 4.3 - - - +
259D GLY* 1.3 73.4 - - - +
261D MET* 1.3 65.7 + - - +
263D ALA* 3.3 2.1 + - - +
264D LEU* 3.0 29.9 + - + +
277D ILE* 4.3 12.6 - - + -
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Residues in contact with MET 261 (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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288C PHE* 3.7 45.9 - - + +
257D THR* 2.9 21.6 + - + +
258D GLU 3.6 7.4 - - - +
260D ALA* 1.3 74.9 - - - +
262D GLN* 1.3 63.2 + - - +
264D LEU* 3.4 18.2 + - + +
265D ASN* 3.5 14.9 + - - +
271D TYR* 3.9 33.2 - - + -
277D ILE* 3.7 24.5 - - + -
285D TRP* 4.6 8.1 - - + -
289D LEU* 4.3 20.2 - - + -
293D LEU* 4.7 5.4 - - - -
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Residues in contact with GLN 262 (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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284C PRO* 4.8 7.3 - - - +
288C PHE* 3.9 20.5 - - + -
231D ASN* 2.8 27.9 + - - +
233D ARG* 3.5 24.4 - - - +
258D GLU* 2.9 22.8 + - - +
259D GLY* 3.1 10.5 + - - +
261D MET* 1.3 76.0 - - - +
263D ALA* 1.3 62.4 + - - +
265D ASN* 3.3 9.8 + - - +
266D VAL* 2.9 25.0 + - + +
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Residues in contact with ALA 263 (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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233D ARG* 3.7 4.0 - - - +
236D ALA* 3.4 34.1 - - + -
237D ILE* 3.6 28.7 - - + +
240D LEU* 4.6 4.7 - - + -
259D GLY 2.7 12.2 + - - +
260D ALA 3.3 5.1 + - - +
262D GLN* 1.3 69.6 - - - +
264D LEU* 1.3 66.4 + - - +
266D VAL* 3.2 2.2 + - - +
267D LEU* 2.9 28.9 + - - +
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Residues in contact with LEU 264 (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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240D LEU* 3.8 15.9 - - + -
249D LEU* 6.2 0.2 - - + -
260D ALA 3.0 19.0 + - - +
261D MET* 3.6 21.5 - - + +
262D GLN 3.3 0.4 - - - -
263D ALA* 1.3 75.2 - - - +
265D ASN* 1.3 60.2 + - + +
267D LEU* 3.1 4.4 + - - +
268D GLY 2.9 7.4 + - - -
269D LEU* 2.7 50.6 + - + +
270D ARG 5.0 0.2 - - - +
271D TYR* 3.7 35.2 - - + +
275D VAL* 3.7 35.9 - - + -
277D ILE* 4.2 11.0 - - + -
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Residues in contact with ASN 265 (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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287C ALA 4.9 8.0 - - - +
288C PHE* 5.1 12.0 - - - +
261D MET 3.5 10.9 + - - +
262D GLN* 3.3 8.9 + - - +
263D ALA 3.3 0.2 - - - -
264D LEU* 1.3 76.7 - - + +
266D VAL* 1.3 69.5 + - - +
267D LEU 3.2 0.2 - - - -
268D GLY* 3.6 11.5 + - - +
269D LEU 4.6 5.8 - - - +
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Residues in contact with VAL 266 (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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233D ARG* 3.4 28.0 - - - +
237D ILE* 3.6 24.7 - - + -
262D GLN* 2.9 20.4 + - + +
263D ALA 3.2 7.6 + - - +
265D ASN* 1.3 79.8 - - - +
267D LEU* 1.3 67.2 + - + +
268D GLY 3.4 0.3 + - - -
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Residues in contact with LEU 267 (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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237D ILE* 4.0 22.4 - - + +
240D LEU* 3.6 33.2 - - + +
241D THR* 3.2 34.1 - - + -
263D ALA 2.9 18.9 + - - +
264D LEU 3.7 3.1 - - - +
266D VAL* 1.3 84.1 - - + +
268D GLY* 1.3 62.7 + - - +
269D LEU* 3.3 22.6 + - + +
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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