Contacts of the helix formed by residues 299 - 317 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C SER* 3.9 12.6 - - - +
297C GLU* 4.3 2.9 - - + +
298C GLN* 1.3 81.3 - - + +
300C THR* 1.3 66.3 + - - +
301C ARG 3.4 2.2 - - - -
302C ARG* 3.3 18.1 + - + -
303C ILE* 2.8 26.2 + - + +
326C LEU* 3.8 22.4 - - + -
327C GLN 3.1 29.6 - - - +
328C THR* 4.4 2.7 - - + -
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Residues in contact with THR 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PHE* 3.7 39.9 - - + +
84C GLU* 2.6 41.6 + - - +
85C VAL* 3.6 12.1 - - - -
281C ASP* 5.6 0.9 - - - +
298C GLN* 2.9 17.0 + - + +
299C PRO* 1.3 71.4 - - - +
301C ARG* 1.3 75.5 + - - +
303C ILE* 3.2 11.7 + - - +
304C GLY 3.1 16.6 + - - -
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Residues in contact with ARG 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLU* 3.5 50.7 + - - +
87C SER* 4.6 1.1 - - - +
88C GLY* 3.5 14.0 - - - +
299C PRO 3.4 0.8 - - - -
300C THR* 1.3 84.3 + - - +
302C ARG* 1.3 58.2 + - - +
304C GLY* 3.1 3.8 + - - -
305C GLN* 2.8 29.7 + - - +
78D GLU* 2.8 46.2 + - - +
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Residues in contact with ARG 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C PRO* 3.3 20.1 + - + +
300C THR 3.2 0.2 - - - -
301C ARG* 1.3 77.1 - - - +
303C ILE* 1.3 66.3 + - - +
305C GLN* 3.6 22.7 + - - -
306C GLU* 2.6 56.4 + - + +
309C ARG* 4.0 7.8 - - - +
324C MET* 5.3 3.2 - - - +
326C LEU* 3.9 19.5 - - + -
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Residues in contact with ILE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PHE* 4.4 19.7 - - + -
85C VAL* 4.3 9.0 - - + -
152C VAL* 3.8 28.9 - - + -
153C ASN* 4.9 3.4 - - - +
164C VAL* 3.9 18.4 - - + +
165C LEU* 5.2 2.5 - - - -
166C SER* 3.5 26.9 - - - +
298C GLN* 4.4 0.4 - - + +
299C PRO* 2.8 33.8 + - + +
300C THR* 3.4 11.7 - - - +
302C ARG* 1.3 76.1 - - - +
304C GLY* 1.3 62.1 + - - +
307C ALA* 3.0 23.9 + - - +
326C LEU* 3.7 21.1 - - + -
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Residues in contact with GLY 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL* 3.3 29.6 - - - +
89C VAL* 3.4 24.6 - - - +
300C THR 3.1 7.1 + - - -
301C ARG 3.1 6.0 + - - -
303C ILE* 1.3 78.0 - - - +
305C GLN* 1.3 61.7 + - - +
307C ALA* 3.5 1.5 + - - +
308C MET* 3.2 20.1 + - - +
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Residues in contact with GLN 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C GLY* 3.6 16.0 - - - +
91C SER* 6.3 1.6 - - - -
92C GLU* 3.1 26.8 + - + +
301C ARG 2.8 19.3 + - - +
302C ARG* 3.6 26.2 + - - +
304C GLY* 1.3 69.9 - - - +
306C GLU* 1.3 57.9 + - - +
308C MET* 3.4 4.2 + - - +
309C ARG* 2.8 65.4 + - - +
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Residues in contact with GLU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C VAL* 4.1 8.7 - - + +
302C ARG* 2.6 68.7 + - + +
303C ILE 4.1 1.3 - - - +
305C GLN* 1.3 73.0 - - - +
307C ALA* 1.3 56.7 + - - +
309C ARG* 3.0 30.2 + - - +
310C MET* 2.7 36.0 + - - +
324C MET* 3.6 39.4 - - + +
326C LEU* 4.3 2.2 - - + -
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Residues in contact with ALA 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ILE* 3.7 13.2 - - + -
150C VAL* 3.5 25.6 - - + +
152C VAL* 3.5 27.8 - - + -
164C VAL* 3.6 12.4 - - + +
303C ILE 3.0 12.3 + - - +
304C GLY 3.9 2.5 - - - +
305C GLN 3.4 0.2 - - - -
306C GLU* 1.3 75.4 - - - +
308C MET* 1.3 53.7 + - - +
310C MET* 3.3 2.8 + - - +
311C LEU* 2.7 34.7 + - - +
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Residues in contact with MET 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C VAL* 3.5 31.6 - - + -
89C VAL* 2.9 37.7 - - + +
92C GLU* 3.8 12.8 - - + -
93C ALA* 3.7 36.8 - - + +
98C TYR* 5.5 1.1 - - - -
100C VAL* 4.7 1.6 - - + -
128C ILE* 3.4 16.3 - - + +
304C GLY 3.2 14.8 + - - +
305C GLN 3.7 3.4 - - - +
307C ALA* 1.3 76.0 - - - +
309C ARG* 1.3 64.5 + - - +
311C LEU* 3.3 7.4 + - - +
312C ILE* 3.0 45.1 + - + +
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Residues in contact with ARG 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU* 3.4 29.1 + - - +
96C LYS* 3.9 14.3 + - - +
302C ARG* 4.0 7.9 - - - +
305C GLN* 2.8 51.9 + - - +
306C GLU* 3.0 39.6 + - - +
308C MET* 1.3 73.6 - - - +
310C MET* 1.3 62.4 + - - +
312C ILE* 3.2 2.3 + - - +
313C HIS* 3.1 37.7 + - + +
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Residues in contact with MET 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C VAL* 3.7 13.7 - - + -
162C GLY* 2.4 44.6 - - - +
163C ALA 4.1 7.0 - - - +
164C VAL* 4.9 5.2 - - + -
306C GLU 2.7 21.5 + - - +
307C ALA* 3.6 6.1 - - - +
309C ARG* 1.3 73.0 - - - +
311C LEU* 1.3 63.2 + - - +
313C HIS* 3.5 9.5 + - - +
314C MET* 3.2 31.9 + - - +
320C ASN 4.1 11.2 - - - +
321C ALA* 3.3 18.6 - - + -
322C THR* 3.3 26.9 - - + +
324C MET* 5.8 5.2 - - - +
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Residues in contact with LEU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C VAL* 3.5 43.7 - - + -
126C GLY* 3.8 11.2 - - - -
127C LEU 3.5 18.2 - - - +
128C ILE* 3.9 13.7 - - + -
148C PRO* 3.5 30.3 - - + +
150C VAL* 3.6 17.4 - - + +
307C ALA 2.7 20.9 + - - +
308C MET* 3.8 9.2 - - - +
309C ARG 3.2 0.2 - - - -
310C MET* 1.3 75.1 - - - +
312C ILE* 1.3 57.8 + - - +
314C MET* 3.2 2.6 + - - +
315C ILE* 2.9 38.5 + - + +
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Residues in contact with ILE 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLU* 4.6 2.0 - - + +
93C ALA* 4.8 0.9 - - - -
96C LYS* 3.5 55.0 - - + +
98C TYR* 4.1 21.3 - - + +
308C MET* 3.0 42.9 + - + +
309C ARG* 3.2 4.9 + - - +
311C LEU* 1.3 73.8 - - - +
313C HIS* 1.3 65.6 + - + +
315C ILE* 3.4 7.5 + - + +
316C GLU* 2.9 55.5 + - + +
318C THR* 5.8 0.4 - - - +
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Residues in contact with HIS 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LYS* 5.8 4.7 + - - -
309C ARG* 3.1 31.7 + - + +
310C MET* 3.8 9.6 - - - +
312C ILE* 1.3 80.1 - - + +
314C MET* 1.3 57.4 + - - +
317C GLY* 2.9 26.3 + - - -
318C THR* 2.8 40.5 + - - -
319C GLY* 3.6 24.5 + - - -
320C ASN 4.8 1.1 - - - +
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Residues in contact with MET 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C PRO* 3.7 30.2 - - + +
149C ILE 3.8 12.1 - - - +
150C VAL* 3.8 12.3 - - - -
160C GLY 3.7 13.2 - - - +
310C MET* 3.2 31.7 + - - +
311C LEU* 3.2 6.7 + - - +
313C HIS* 1.3 76.7 - - - +
315C ILE* 1.3 61.7 + - - +
317C GLY* 3.6 7.6 + - - -
319C GLY 3.9 7.9 - - - +
320C ASN 4.1 4.0 - - - -
321C ALA* 3.5 45.1 - - + +
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Residues in contact with ILE 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ARG 4.7 7.4 - - - +
70C VAL* 3.9 14.8 - - + -
98C TYR* 3.7 23.6 - - + +
125C ASP* 3.7 50.5 - - + +
148C PRO* 3.8 11.2 - - + -
311C LEU* 2.9 39.0 + - + +
312C ILE* 3.7 6.7 - - + +
314C MET* 1.3 79.1 - - - +
316C GLU* 1.3 63.0 + - + +
317C GLY 3.2 1.6 + - - -
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Residues in contact with GLU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ASN* 5.3 0.3 + - - -
96C LYS* 5.5 0.5 - - - +
98C TYR* 2.7 39.6 + - - +
312C ILE* 2.9 32.3 + - - +
313C HIS 4.5 0.7 - - - +
315C ILE* 1.3 74.5 - - + +
317C GLY* 1.3 64.3 + - - +
318C THR* 3.4 21.1 + - + +
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Residues in contact with GLY 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C HIS 2.9 6.1 + - - -
314C MET 3.6 6.9 + - - -
315C ILE 3.2 5.3 + - - -
316C GLU* 1.3 79.1 - - - +
318C THR* 1.3 60.3 + - - +
319C GLY 3.6 4.7 - - - -
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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