Contacts of the helix formed by residues 5 - 20 (chain 4) in PDB entry 3EXG
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 VAL 5 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44 THR* 1.3 71.2 - - - +
64 ARG* 1.3 65.1 + - - +
84 ALA* 3.2 14.8 + - - +
94 ILE* 3.3 14.5 + - + +
1474 PRO* 6.1 0.9 - - + -
1484 TRP 3.7 14.1 - - - +
1494 ASN* 3.7 7.6 - - - +
1504 SER* 3.5 27.8 + - - +
1534 ALA* 3.6 24.7 - - + -
1714 GLU* 6.5 0.4 - - + -
1754 MET* 3.0 31.0 - - + +
1764 TYR* 3.6 6.5 + - + -
1784 VAL 3.1 11.8 + - - +
1804 PHE* 4.0 5.4 - - + -
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Residues in contact with ARG 6 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44 THR* 3.0 10.7 + - - +
54 VAL* 1.3 78.8 - - - +
74 ASP* 1.3 75.4 + - - +
94 ILE* 3.2 13.6 + - - +
104 ASN* 3.2 9.8 + - + +
374 TYR* 2.8 22.8 + - - +
384 LYS* 3.1 32.3 - - - +
394 VAL* 4.1 12.7 - - + +
414 ARG* 4.2 8.7 - - - +
1764 TYR* 2.8 61.8 + - + +
1774 GLY* 4.0 9.9 - - - +
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Residues in contact with ASP 7 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34 VAL* 5.2 6.0 - - + +
44 THR* 2.9 27.5 + - - +
64 ARG* 1.3 91.3 + - - +
84 ALA* 1.3 68.6 + - - +
104 ASN* 2.7 22.9 + - + +
114 GLN* 2.7 25.3 + - - +
384 LYS 5.2 0.2 - - - +
414 ARG* 5.2 3.6 + - - -
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Residues in contact with ALA 8 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34 VAL* 4.4 9.0 - - + +
44 THR 3.1 13.4 + - - +
54 VAL 3.2 10.7 + - - +
74 ASP* 1.3 77.0 - - - +
94 ILE* 1.3 61.3 + - - +
114 GLN* 3.7 6.0 + - - +
124 GLY 3.3 8.7 + - - -
1504 SER* 3.4 40.4 - - - +
1534 ALA* 4.5 0.9 - - + -
1544 LYS* 3.0 26.9 - - + +
1824 PHE* 4.6 6.3 - - + -
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Residues in contact with ILE 9 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54 VAL* 3.8 11.4 - - + +
64 ARG 3.2 6.6 + - - +
74 ASP 3.0 0.4 - - - -
84 ALA* 1.3 74.1 - - - +
104 ASN* 1.3 68.5 + - - +
124 GLY* 2.8 14.0 + - - -
134 MET* 2.9 33.6 + - + +
394 VAL* 3.8 19.1 - - + -
1154 ARG* 4.4 1.1 - - - +
1474 PRO* 6.0 0.4 - - + -
1534 ALA* 3.7 30.1 - - + +
1574 ILE* 4.3 16.9 - - + +
1714 GLU* 3.4 39.0 - - + +
1764 TYR* 4.1 16.2 - - + -
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Residues in contact with ASN 10 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64 ARG* 3.2 8.4 + - + +
74 ASP* 2.7 17.6 + - - +
94 ILE* 1.3 81.6 - - - +
114 GLN* 1.3 59.8 + - - +
134 MET* 3.9 6.1 - - - +
144 ASP* 3.3 23.4 + - - +
384 LYS 5.6 0.2 - - - +
394 VAL 3.1 27.9 + - - +
404 SER* 3.5 13.9 - - - +
414 ARG* 3.6 8.7 + - - +
434 LEU* 3.3 31.0 - - - +
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Residues in contact with GLN 11 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34 VAL* 5.5 6.7 - - - +
74 ASP* 2.7 24.2 + - - +
84 ALA* 3.7 9.6 - - - +
104 ASN* 1.3 72.4 + - - +
124 GLY* 1.3 69.1 + - - +
144 ASP* 2.8 18.9 + - + +
154 GLU* 2.9 26.5 + - + +
1544 LYS* 2.8 30.2 + - - +
1824 PHE* 3.6 19.1 - - - -
1874 GLN* 4.1 9.4 - - - +
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Residues in contact with GLY 12 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84 ALA 3.3 4.9 + - - -
94 ILE 2.8 11.5 + - - -
114 GLN* 1.3 77.0 - - - +
134 MET* 1.3 61.2 + - - -
154 GLU* 3.4 1.7 + - - -
164 GLU* 3.2 26.8 + - - +
1544 LYS* 4.1 3.9 - - - +
1574 ILE* 4.0 11.4 - - - -
1584 LYS* 3.6 31.7 - - - +
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Residues in contact with MET 13 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94 ILE* 2.9 36.8 + - + +
104 ASN* 3.9 4.7 - - - +
124 GLY* 1.3 72.3 - - - -
144 ASP* 1.3 55.2 + - - +
164 GLU* 3.3 1.7 + - - +
174 LEU* 2.8 43.0 + - + +
254 LEU* 4.3 18.2 - - + -
394 VAL* 3.9 17.5 - - + +
404 SER* 4.3 7.6 - - - -
434 LEU* 4.3 11.7 - - + -
774 ILE* 3.9 34.3 - - + -
1154 ARG* 3.5 36.1 - - - +
1574 ILE* 4.4 9.5 - - + +
1614 ILE* 4.5 10.3 - - - +
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Residues in contact with ASP 14 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104 ASN* 3.3 16.2 + - - +
114 GLN* 2.8 14.8 + - + +
134 MET* 1.3 80.7 - - - +
154 GLU* 1.3 62.4 + - + +
174 LEU* 3.4 4.2 + - - -
184 GLU* 3.1 19.8 + - - +
434 LEU* 4.5 16.4 - - + +
464 LYS* 3.0 24.0 + - - +
474 TYR* 2.7 37.3 + - - -
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Residues in contact with GLU 15 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114 GLN* 2.9 21.9 + - + +
124 GLY 4.1 0.4 - - - +
144 ASP* 1.3 78.9 - - + +
164 GLU* 1.3 57.6 + - - +
184 GLU* 3.5 5.8 + - - +
194 ARG* 2.9 31.3 + - - +
1544 LYS* 3.2 34.2 + - - -
1584 LYS* 3.3 27.0 + - - +
1874 GLN 3.7 5.2 - - - +
1894 LYS* 3.4 44.5 - - + +
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Residues in contact with GLU 16 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124 GLY 3.2 18.4 + - - +
134 MET 3.7 1.3 - - - +
154 GLU* 1.3 73.6 - - - +
174 LEU* 1.3 67.8 + - - +
194 ARG* 2.8 32.9 + - - +
204 ASP* 2.9 27.8 + - - +
234 VAL* 4.4 5.9 - - + +
1584 LYS* 2.7 29.4 + - + +
1614 ILE* 3.7 43.9 - - + +
1624 ARG* 2.5 37.2 + - - +
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Residues in contact with LEU 17 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134 MET* 2.8 24.0 + - + +
144 ASP 3.6 5.4 - - - +
164 GLU* 1.3 77.7 - - - +
184 GLU* 1.3 59.5 + - - +
204 ASP 3.3 5.0 - - - +
234 VAL* 3.1 39.0 - - + +
244 PHE* 4.1 8.3 - - - -
254 LEU* 5.2 6.3 - - + -
434 LEU* 4.2 16.6 - - + -
474 TYR* 3.7 26.2 - - + -
514 ARG* 2.4 48.5 + - + +
524 ILE* 3.9 22.9 - - + -
774 ILE* 5.2 2.9 - - + -
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Residues in contact with GLU 18 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144 ASP 3.1 15.8 + - - +
154 GLU* 3.8 6.1 - - - +
164 GLU 3.1 0.4 - - - -
174 LEU* 1.3 73.3 - - - +
194 ARG* 1.3 67.1 + - - +
204 ASP* 3.2 4.1 + - - -
214 GLU 5.1 0.2 + - - -
464 LYS* 2.9 35.7 + - - -
474 TYR* 3.7 10.2 + - + +
1894 LYS* 6.5 0.7 - - - -
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Residues in contact with ARG 19 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154 GLU 2.9 19.5 + - - +
164 GLU* 2.8 29.1 + - - +
184 GLU* 1.3 80.1 - - - +
204 ASP* 1.3 68.9 + - + +
214 GLU* 5.4 0.2 - - - +
234 VAL* 6.2 0.2 - - - +
1624 ARG* 3.3 49.9 - - - +
1894 LYS* 4.4 22.4 - - - +
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Residues in contact with ASP 20 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164 GLU 2.9 10.0 + - - +
174 LEU 3.3 5.2 - - - +
184 GLU 3.2 2.7 - - - -
194 ARG* 1.3 91.3 - - + +
214 GLU* 1.3 68.4 + - - +
224 LYS* 2.6 49.2 + - - +
234 VAL* 3.1 25.4 + - + +
514 ARG* 3.2 9.9 + - - -
754 ARG* 3.4 17.0 - - - -
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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
------------------------------------------------------------
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