Contacts of the helix formed by residues 299 - 317 (chain F) 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 PRO 299 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F SER* 4.0 11.2 - - - +
297F GLU* 4.3 2.2 - - - +
298F GLN* 1.3 82.4 - - + +
300F THR* 1.3 58.7 + - - +
301F ARG 3.3 2.9 - - - -
302F ARG* 3.0 20.3 + - + -
303F ILE* 2.8 29.2 + - + +
326F LEU* 3.7 24.9 - - + -
327F GLN 3.0 31.6 - - - +
328F THR* 4.2 2.7 - - + -
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Residues in contact with THR 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F PHE* 3.7 40.6 - - + +
84F GLU* 2.7 41.6 + - - +
85F VAL* 3.4 15.3 - - - +
281F ASP* 5.7 0.7 - - - +
298F GLN* 2.8 23.2 + - + +
299F PRO* 1.3 71.4 - - - +
301F ARG* 1.3 72.6 + - - +
303F ILE* 3.4 8.7 + - - -
304F GLY 3.2 16.5 + - - -
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Residues in contact with ARG 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E GLU* 2.6 48.5 + - - +
84F GLU* 3.4 47.9 + - - +
87F SER* 4.5 4.7 - - - +
88F GLY* 3.5 13.6 - - - +
299F PRO 3.3 0.4 - - - -
300F THR* 1.3 83.2 + - - +
302F ARG* 1.3 57.8 + - - +
304F GLY* 3.1 4.5 + - - -
305F GLN* 2.9 27.2 + - - +
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Residues in contact with ARG 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F PRO* 3.0 20.3 + - + +
301F ARG* 1.3 75.8 - - - +
303F ILE* 1.3 60.2 + - - +
305F GLN* 3.6 23.5 + - - -
306F GLU* 2.6 67.6 + - + +
309F ARG* 4.3 6.6 - - - +
324F MET* 5.4 3.4 - - - +
326F LEU* 3.9 19.5 - - + +
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Residues in contact with ILE 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F PHE* 4.5 18.2 - - + -
85F VAL* 4.3 9.2 - - + -
152F VAL* 3.7 20.4 - - + -
153F ASN* 4.8 4.3 - - - +
164F VAL* 3.7 28.4 - - + +
165F LEU 4.8 2.2 - - - +
166F SER* 3.6 27.1 - - - +
298F GLN* 4.6 0.2 - - - +
299F PRO* 2.8 31.7 + - + +
300F THR* 3.5 12.1 - - - +
301F ARG 3.3 0.2 - - - -
302F ARG* 1.3 75.4 - - - +
304F GLY* 1.3 64.3 + - - +
307F ALA* 3.1 22.5 + - - +
326F LEU* 3.6 23.1 - - + -
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Residues in contact with GLY 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F VAL* 3.2 30.9 - - - +
89F VAL* 3.3 23.4 - - - +
300F THR 3.2 5.3 + - - -
301F ARG 3.1 5.7 + - - -
303F ILE* 1.3 79.1 - - - +
305F GLN* 1.3 60.9 + - - +
307F ALA* 3.2 2.7 + - - +
308F MET* 3.0 20.8 + - - +
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Residues in contact with GLN 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F GLY* 3.6 17.5 - - - +
91F SER* 6.2 1.8 - - - -
92F GLU* 3.3 29.5 + - - +
301F ARG 2.9 18.3 + - - +
302F ARG* 3.6 28.7 + - - +
304F GLY* 1.3 70.9 - - - +
306F GLU* 1.3 59.9 + - - +
308F MET 3.4 2.1 + - - -
309F ARG* 2.8 62.5 + - - +
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Residues in contact with GLU 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F VAL* 4.0 16.9 - - + +
302F ARG* 2.6 67.2 + - + +
305F GLN* 1.3 74.8 - - - +
307F ALA* 1.3 55.2 + - - +
309F ARG* 3.2 29.4 + - - +
310F MET* 2.6 36.6 + - - +
324F MET* 3.5 36.2 - - + +
326F LEU* 4.3 3.8 - - + -
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Residues in contact with ALA 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F ILE* 3.9 11.9 - - + -
150F VAL* 3.7 19.7 - - + +
152F VAL* 3.5 24.5 - - + -
164F VAL* 3.7 12.3 - - + +
303F ILE 3.1 18.2 + - - +
304F GLY* 3.6 4.7 - - - +
306F GLU* 1.3 79.0 - - - +
308F MET* 1.3 57.4 + - - +
310F MET* 3.7 1.0 - - - -
311F LEU* 2.7 29.6 + - - +
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Residues in contact with MET 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F VAL* 3.7 34.1 - - + -
89F VAL* 2.7 39.0 - - + +
92F GLU* 3.9 9.0 - - + -
93F ALA* 3.6 35.4 - - + +
98F TYR* 5.6 1.1 - - - -
100F VAL* 4.1 3.1 - - + -
128F ILE* 3.5 12.2 - - + +
304F GLY 3.0 15.7 + - - +
305F GLN 3.7 4.0 - - - +
307F ALA* 1.3 79.6 - - - +
309F ARG* 1.3 55.0 + - - +
311F LEU* 3.8 8.2 - - - +
312F ILE* 3.0 54.9 + - + +
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Residues in contact with ARG 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F GLU* 3.4 34.9 + - - +
96F LYS* 3.8 8.4 + - - +
302F ARG* 4.3 6.5 - - - +
305F GLN* 2.8 47.6 + - - +
306F GLU* 3.1 37.6 + - - +
308F MET* 1.3 70.8 - - - +
310F MET* 1.3 64.1 + - - +
312F ILE* 3.4 6.2 + - - +
313F HIS* 2.9 39.9 + - + +
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Residues in contact with MET 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F VAL* 3.9 13.5 - - + -
162F GLY* 2.3 46.9 - - - +
163F ALA 4.2 6.3 - - - +
164F VAL* 4.7 6.3 - - + -
306F GLU* 2.6 21.0 + - - +
307F ALA* 3.9 3.6 - - - +
309F ARG* 1.3 72.8 - - - +
311F LEU* 1.3 62.7 + - - +
313F HIS* 3.6 9.0 + - - +
314F MET* 3.1 32.1 + - - +
320F ASN 4.0 14.8 - - - +
321F ALA* 3.5 6.3 - - + -
322F THR* 3.1 38.6 - - + +
324F MET* 5.6 7.9 - - - +
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Residues in contact with LEU 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F VAL* 3.4 44.4 - - + -
126F GLY 3.9 0.7 - - - -
127F LEU 3.7 15.7 - - - +
128F ILE* 3.8 12.6 - - + -
148F PRO* 3.4 42.4 - - + +
150F VAL* 3.7 22.2 - - + +
307F ALA 2.7 21.7 + - - +
308F MET* 3.8 9.0 - - - +
309F ARG 3.2 0.2 - - - -
310F MET* 1.3 74.3 - - - +
312F ILE* 1.3 58.0 + - - +
314F MET* 3.2 5.3 + - - +
315F ILE* 2.9 37.2 + - + +
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Residues in contact with ILE 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F GLU* 4.5 2.5 - - + +
93F ALA* 4.8 0.4 - - - -
96F LYS* 3.7 50.0 - - + +
98F TYR* 4.1 20.0 - - + -
308F MET* 3.0 43.2 + - + +
309F ARG 3.9 4.7 - - - +
310F MET 3.3 0.2 - - - -
311F LEU* 1.3 74.4 - - + +
313F HIS* 1.3 70.1 + - + +
315F ILE* 4.4 7.2 - - + -
316F GLU* 2.9 54.3 + - + +
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Residues in contact with HIS 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F LYS* 5.7 6.5 + - - -
309F ARG* 2.9 35.3 + - + +
310F MET* 3.9 8.7 - - - +
312F ILE* 1.3 80.7 - - + +
314F MET* 1.3 57.1 + - - +
317F GLY* 2.7 28.4 + - - -
318F THR* 2.8 41.5 + - - +
319F GLY* 3.7 21.5 + - - -
320F ASN 5.5 0.9 - - - +
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Residues in contact with MET 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F PRO* 3.4 37.0 - - + +
149F ILE 3.8 9.2 - - - +
150F VAL* 4.0 20.2 - - - -
160F GLY 3.9 18.6 - - - +
310F MET* 3.1 20.9 + - - +
311F LEU* 3.2 7.2 + - - +
313F HIS* 1.3 78.1 - - - +
315F ILE* 1.3 60.7 + - - +
317F GLY* 3.8 6.5 + - - -
319F GLY 4.1 6.5 - - - +
320F ASN* 4.0 5.8 - - - -
321F ALA* 3.7 33.7 - - + +
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Residues in contact with ILE 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ARG 4.8 8.1 - - - +
70F VAL* 3.9 21.5 - - + -
98F TYR* 3.8 23.3 - - + +
125F ASP* 3.6 51.1 - - + +
148F PRO* 4.0 9.9 - - + -
311F LEU* 2.9 28.3 + - + +
312F ILE* 3.7 7.6 - - + +
313F HIS 3.2 0.2 - - - -
314F MET* 1.3 76.0 - - - +
316F GLU* 1.3 61.3 + - + +
317F GLY* 3.2 5.6 + - - -
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Residues in contact with GLU 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F ASN* 5.4 0.2 + - - -
96F LYS* 5.3 3.1 - - - +
98F TYR* 2.8 40.8 + - - +
312F ILE* 2.9 29.5 + - - +
313F HIS 4.5 0.2 - - - +
315F ILE* 1.3 77.7 - - + +
317F GLY* 1.3 64.3 + - - +
318F THR* 3.3 21.1 + - + +
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Residues in contact with GLY 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F HIS 2.7 10.3 + - - -
314F MET 3.8 5.3 + - - -
315F ILE 3.2 4.8 + - - -
316F GLU* 1.3 80.5 - - - +
318F THR* 1.3 58.9 + - - +
319F GLY 3.5 5.4 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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