Contacts of the helix formed by residues 299 - 316 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B SER* 4.0 12.1 - - - +
297B GLU* 4.4 2.9 - - + +
298B GLN* 1.3 80.5 - - + +
300B THR* 1.3 59.5 + - - +
301B ARG 3.3 2.7 - - - -
302B ARG* 3.1 18.1 + - + -
303B ILE* 2.9 29.1 + - + +
326B LEU* 3.7 24.7 - - + +
327B GLN 3.3 29.2 - - - +
328B THR* 4.4 1.3 - - + -
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 3.6 42.8 - - + +
84B GLU* 2.6 42.6 + - - +
85B VAL* 3.4 14.4 - - - +
281B ASP* 5.7 0.4 - - - +
298B GLN* 2.8 20.4 + - + +
299B PRO* 1.3 71.2 - - - +
301B ARG* 1.3 70.4 + - - +
303B ILE* 3.4 8.8 + - - -
304B GLY 3.2 15.4 + - - -
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.8 46.0 + - - +
84B GLU* 3.4 50.7 + - - +
87B SER* 4.6 0.9 - - - +
88B GLY* 3.5 15.8 - - - +
299B PRO 3.3 0.6 - - - -
300B THR* 1.3 84.7 + - - +
302B ARG* 1.3 58.9 + - - +
304B GLY 3.2 1.4 + - - -
305B GLN* 2.9 30.3 + - - +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PRO* 3.1 19.4 + - + +
301B ARG* 1.3 77.9 - - - +
303B ILE* 1.3 59.2 + - - +
305B GLN* 3.6 22.4 + - - -
306B GLU* 2.7 66.4 + - + +
309B ARG* 3.8 8.1 - - - +
324B MET* 5.5 2.5 - - - +
326B LEU* 4.0 15.0 - - + -
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Residues in contact with ILE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PHE* 4.4 19.7 - - + -
85B VAL* 4.3 9.0 - - + -
152B VAL* 3.8 28.5 - - + -
153B ASN* 4.9 3.8 - - - +
164B VAL* 3.8 18.4 - - + +
165B LEU* 5.2 2.5 - - - -
166B SER* 3.4 26.9 - - - +
298B GLN* 4.5 0.7 - - + +
299B PRO* 2.9 29.9 + - + +
300B THR* 3.5 12.3 - - - +
302B ARG* 1.3 73.2 - - - +
304B GLY* 1.3 58.7 + - - +
306B GLU 3.5 0.2 + - - -
307B ALA* 2.9 29.6 + - - +
326B LEU* 3.7 22.9 - - + +
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Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 3.2 30.9 - - - +
89B VAL* 3.4 27.4 - - - +
300B THR 3.2 5.1 + - - -
301B ARG 3.2 5.4 + - - -
302B ARG 3.2 0.6 - - - -
303B ILE* 1.3 79.1 - - - +
305B GLN* 1.3 61.2 + - - +
307B ALA* 3.3 2.0 + - - +
308B MET* 3.2 17.8 + - - +
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Residues in contact with GLN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLY* 3.5 17.9 - - - +
91B SER* 5.9 2.2 + - - -
92B GLU* 3.4 23.3 + - + +
301B ARG 2.9 19.4 + - - +
302B ARG* 3.6 23.6 + - - +
304B GLY* 1.3 71.2 - - - +
306B GLU* 1.3 58.2 - - - +
308B MET* 3.5 3.1 + - - +
309B ARG* 2.8 67.3 + - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL* 4.1 9.1 - - + +
302B ARG* 2.7 67.3 + - + +
303B ILE 4.1 2.5 - - - +
305B GLN* 1.3 71.3 - - - +
307B ALA* 1.3 61.2 + - - +
309B ARG* 2.9 29.1 + - - +
310B MET* 2.9 29.6 + - - +
324B MET* 3.4 42.8 - - + +
326B LEU* 4.4 2.7 - - + -
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 3.6 14.6 - - + -
150B VAL* 3.5 26.2 - - + +
152B VAL* 3.6 20.9 - - + -
164B VAL* 3.8 9.6 - - + +
303B ILE 2.9 19.9 + - - +
304B GLY 3.3 2.4 + - - +
306B GLU* 1.3 76.3 - - - +
308B MET* 1.3 54.7 + - - +
310B MET* 3.3 1.8 + - - -
311B LEU* 2.8 35.5 + - - +
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Residues in contact with MET 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 3.6 35.0 - - + -
89B VAL* 2.9 48.9 - - + +
92B GLU* 3.8 15.0 - - + -
93B ALA* 3.7 17.9 - - + +
98B TYR* 5.6 0.9 - - - -
100B VAL* 4.3 1.8 - - + -
128B ILE* 3.4 9.8 - - + +
304B GLY 3.2 14.2 + - - +
305B GLN 3.7 3.8 - - - +
307B ALA* 1.3 78.4 - - - +
309B ARG* 1.3 57.2 + - - +
311B LEU* 3.2 8.5 + - - -
312B ILE* 2.9 57.3 + - + +
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Residues in contact with ARG 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLU* 3.4 31.1 + - - +
96B LYS* 3.9 14.1 + - - +
302B ARG* 3.8 9.1 - - - +
305B GLN* 2.8 48.1 + - - +
306B GLU* 2.9 38.9 + - - +
307B ALA 3.4 0.2 - - - -
308B MET* 1.3 76.3 - - - +
310B MET* 1.3 61.3 + - - +
312B ILE* 3.4 1.9 + - - +
313B HIS* 3.0 37.4 + - + +
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Residues in contact with MET 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL* 4.3 9.2 - - + -
162B GLY* 2.6 36.3 - - - -
163B ALA 4.2 7.4 - - - +
164B VAL* 4.8 5.4 - - + -
306B GLU 2.9 21.8 + - - +
307B ALA* 3.8 3.4 - - - +
309B ARG* 1.3 72.7 - - - +
311B LEU* 1.3 63.4 + - - +
313B HIS* 3.5 10.2 + - - +
314B MET* 3.0 34.1 + - - +
320B ASN 3.9 14.4 - - - +
321B ALA* 3.0 8.1 - - + -
322B THR* 2.5 49.4 - - + +
324B MET* 5.7 5.4 - - - +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B VAL* 3.4 44.4 - - + -
126B GLY* 3.7 11.9 - - - -
127B LEU 3.6 12.1 - - - +
128B ILE* 3.8 12.3 - - + -
148B PRO* 3.3 40.2 - - + +
150B VAL* 3.7 15.0 - - + +
307B ALA 2.8 21.6 + - - +
308B MET* 3.2 8.5 + - - +
310B MET* 1.3 72.9 - - - +
312B ILE* 1.3 58.4 + - - +
314B MET* 3.3 4.5 + - - +
315B ILE* 2.9 38.2 + - + +
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B GLU* 4.6 1.1 - - + +
93B ALA* 4.8 0.7 - - - -
96B LYS* 3.6 55.6 - - + +
98B TYR* 4.0 22.0 - - + +
308B MET* 2.9 43.3 + - + +
309B ARG 3.8 4.3 - - - +
311B LEU* 1.3 74.7 - - - +
313B HIS* 1.3 63.6 + - + +
315B ILE* 3.7 7.3 - - + +
316B GLU* 3.0 57.4 + - - +
318B THR* 5.8 0.2 - - - +
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Residues in contact with HIS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS* 5.7 4.7 + - - -
309B ARG* 3.0 33.1 + - + +
310B MET* 3.7 10.3 - - - +
312B ILE* 1.3 79.6 - - + +
314B MET* 1.3 56.2 + - - +
317B GLY* 2.9 10.0 + - - -
318B THR* 2.7 57.5 + - - -
319B GLY* 3.3 23.5 + - - -
320B ASN 4.9 1.3 - - - +
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Residues in contact with MET 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PRO* 3.7 30.1 - - + +
149B ILE 3.6 18.8 - - - +
150B VAL* 3.7 22.0 - - - -
160B GLY 3.7 8.3 - - - +
310B MET* 3.0 24.2 + - - +
311B LEU* 3.6 6.5 - - - +
313B HIS* 1.3 75.5 - - - +
315B ILE* 1.3 63.8 + - - +
317B GLY* 3.5 8.0 + - - -
319B GLY 3.8 7.4 - - - +
320B ASN 4.1 3.4 - - - -
321B ALA* 3.5 47.3 - - + +
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ARG 4.6 8.7 - - - +
70B VAL* 3.8 22.7 - - + -
98B TYR* 3.9 22.0 - - + +
125B ASP* 3.5 51.1 - - + +
148B PRO* 3.8 11.9 - - + -
311B LEU* 2.9 32.8 + - + +
312B ILE* 3.2 7.6 + - + +
314B MET* 1.3 77.2 - - - +
316B GLU* 1.3 63.2 + - + +
317B GLY* 3.2 1.0 + - - -
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 5.4 0.5 + - - -
96B LYS* 5.6 1.0 - - - +
98B TYR* 2.6 38.8 + - - +
312B ILE* 3.0 27.1 + - - +
313B HIS 4.6 0.4 - - - +
315B ILE* 1.3 79.7 - - + +
317B GLY* 1.3 62.2 + - - +
318B THR* 3.3 22.1 + - + +
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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
------------------------------------------------------------
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