Contacts of the helix formed by residues 58 - 72 (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 SER 58 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1773 GLU* 2.9 36.8 + - - +
1803 ASN* 5.1 0.3 + - - -
1813 MET* 4.3 12.2 - - - +
284 GLU* 4.0 1.4 + - - -
564 PRO* 3.0 18.7 + - - +
574 ILE* 1.3 73.1 + - - +
594 GLU* 1.3 68.5 + - - +
624 PHE* 2.9 19.9 + - - -
1715 ASN* 2.8 30.0 + - - +
1725 GLN* 4.1 3.4 - - - +
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Residues in contact with GLU 59 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1773 GLU* 3.8 0.2 + - - -
284 GLU* 2.8 28.1 - - - +
574 ILE* 4.1 6.4 - - - +
584 SER* 1.3 69.1 + - - +
604 MET* 1.3 68.6 + - - +
614 GLY 2.9 0.2 + - - -
624 PHE* 3.5 23.3 - - + -
634 ALA* 2.8 28.2 + - - +
804 PHE* 4.2 10.3 - - + -
814 MET* 5.5 1.7 + - - +
854 PHE* 3.6 44.5 - - + +
884 GLN* 3.6 11.1 + - + +
894 ALA* 3.8 9.6 - - + -
1725 GLN* 3.6 19.7 + - - +
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Residues in contact with MET 60 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433 PRO* 4.7 0.2 - - - +
1743 GLN* 3.4 35.4 - - + +
1773 GLU* 3.3 13.9 + - - +
594 GLU* 1.3 78.6 - - - +
614 GLY* 1.3 60.9 + - - +
644 GLY* 3.2 15.4 + - - -
884 GLN* 3.4 36.3 + - + +
894 ALA* 3.8 10.6 - - - +
914 ASP* 4.8 11.0 - - + +
924 GLN* 3.6 26.9 + - - +
606 MET* 5.8 3.4 - - + -
886 GLN* 3.9 49.1 - - + +
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Residues in contact with GLY 61 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433 PRO* 3.7 15.8 - - - +
1743 GLN 4.8 0.2 - - - -
1773 GLU* 2.5 36.7 + - - -
1783 ALA 5.2 0.4 - - - -
1813 MET* 3.9 9.0 - - - -
584 SER 3.5 0.9 - - - -
604 MET* 1.3 72.8 - - - +
624 PHE* 1.3 60.2 + - - +
644 GLY* 3.2 2.9 + - - -
654 ILE* 2.8 29.5 + - - +
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Residues in contact with PHE 62 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1813 MET* 3.8 19.8 - - - +
264 LEU* 4.4 13.6 - - + +
274 GLY* 4.3 8.1 - - - -
284 GLU* 3.7 16.4 - - - -
554 THR* 3.6 36.3 - - + -
564 PRO 4.0 3.1 - - - -
584 SER* 2.9 27.2 + - - -
594 GLU* 3.5 33.2 - - + -
614 GLY* 1.3 72.7 - - - +
634 ALA* 1.3 69.7 + - - +
654 ILE* 3.6 6.4 - - + +
664 ALA* 2.8 24.1 + - - +
784 CYS* 3.8 22.7 - - - -
794 GLU 3.9 20.6 - - - -
804 PHE* 4.6 7.2 - + - -
814 MET 5.9 0.4 - - - -
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Residues in contact with ALA 63 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594 GLU 2.8 21.6 + - - +
604 MET 3.9 2.0 - - - +
624 PHE* 1.3 77.6 - - - +
644 GLY* 1.3 65.5 + - - +
664 ALA* 3.1 2.8 + - - +
674 VAL* 3.0 22.6 + - - +
784 CYS* 4.2 12.6 - - - -
804 PHE* 4.2 15.3 - - + -
894 ALA* 3.4 23.6 - - + +
924 GLN* 4.0 12.6 - - + -
934 VAL* 5.3 0.2 - - + -
1144 PHE* 4.8 6.8 - - + -
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Residues in contact with GLY 64 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433 PRO* 3.8 11.8 - - - +
1443 LEU* 3.7 7.7 - - - +
604 MET 3.2 9.1 + - - -
614 GLY 3.2 3.8 + - - -
634 ALA* 1.3 76.4 - - - +
654 ILE* 1.3 64.6 + - - +
674 VAL* 2.9 14.5 + - - +
684 GLY* 2.9 10.9 + - - -
924 GLN* 3.6 30.7 - - - +
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Residues in contact with ILE 65 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1433 PRO* 3.7 20.9 + - + +
1463 ALA* 4.0 21.8 - - + +
1473 GLY* 3.2 13.4 - - - +
1503 LEU* 4.3 21.5 - - + -
1783 ALA* 5.3 2.0 - - + -
1813 MET* 3.7 33.4 - - + -
1853 TRP* 4.0 20.9 - - + -
1873 LEU* 5.2 2.2 - - + -
264 LEU* 4.4 11.7 - - + -
614 GLY 2.8 17.3 + - - +
624 PHE* 3.2 8.7 + - - +
644 GLY* 1.3 71.4 - - - +
664 ALA* 1.3 65.0 + - - +
694 ALA* 3.0 19.1 + - - +
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Residues in contact with ALA 66 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244 PHE* 5.4 1.1 - - - -
264 LEU* 3.7 27.1 - - + +
624 PHE 2.8 16.8 + - - +
634 ALA 3.6 6.7 - - - +
644 GLY 3.1 0.2 + - - -
654 ILE* 1.3 75.5 - - - +
674 VAL* 1.3 63.8 + - - +
684 GLY 3.1 0.3 + - - -
694 ALA* 3.1 9.3 + - - +
704 ALA 2.9 18.9 + - - -
764 PRO* 3.5 12.8 - - + +
784 CYS* 4.0 8.3 - - + -
1124 ILE* 3.7 17.5 - - + -
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Residues in contact with VAL 67 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1443 LEU* 4.0 16.2 - - + -
634 ALA 3.0 15.2 + - - +
644 GLY 2.9 7.1 + - - +
664 ALA* 1.3 76.3 - - - +
684 GLY* 1.3 57.5 + - - +
704 ALA* 3.3 3.8 + - - +
714 MET* 2.9 33.4 + - - +
924 GLN* 4.4 11.7 - - + +
964 SER* 4.3 3.1 - - - -
974 ALA* 4.0 24.7 - - + +
1104 VAL* 3.7 19.1 - - + -
1124 ILE* 3.7 20.0 - - + -
1144 PHE* 3.8 13.9 - - + -
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Residues in contact with GLY 68 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1443 LEU* 3.6 29.3 - - - +
1483 ILE* 3.6 12.8 - - - +
644 GLY 2.9 10.6 + - - -
654 ILE 3.6 3.6 - - - -
674 VAL* 1.3 75.2 - - - +
694 ALA* 1.3 66.6 + - - +
714 MET* 3.2 9.2 + - - +
724 ALA* 2.9 23.2 + - - +
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Residues in contact with ALA 69 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1473 GLY 3.6 16.7 - - - +
1503 LEU* 4.8 5.6 - - + -
1513 ALA* 4.3 9.5 - - + +
244 PHE* 3.9 32.1 - - + -
654 ILE 3.0 11.7 + - - +
664 ALA* 3.2 10.1 - - - +
684 GLY* 1.3 73.2 - - - +
704 ALA* 1.3 63.9 + - - +
724 ALA* 3.1 11.3 + - - +
734 GLY 3.3 0.5 + - - -
744 LEU* 3.1 22.3 + - + +
764 PRO* 4.7 0.7 - - + -
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Residues in contact with ALA 70 (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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664 ALA 2.9 12.0 + - - +
674 VAL 3.5 9.2 - - - +
694 ALA* 1.3 74.6 - - - +
714 MET* 1.3 60.2 + - - +
734 GLY* 2.9 19.4 + - - -
744 LEU 3.3 17.1 - - - +
764 PRO* 3.8 16.4 - - + +
1104 VAL* 3.8 19.3 - - + -
1114 PRO* 3.7 28.1 - - + +
1124 ILE* 4.0 3.4 - - + +
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Residues in contact with MET 71 (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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1273 TYR* 4.1 4.3 - - + -
1323 TYR* 3.8 45.0 - - + +
1353 ASN* 5.2 1.1 - - - +
1443 LEU* 4.2 24.5 - - + -
1483 ILE* 5.2 1.6 - - + -
674 VAL* 2.9 23.3 + - - +
684 GLY* 3.4 10.8 - - - +
704 ALA* 1.3 77.7 - - - +
724 ALA* 1.3 58.2 + - - +
734 GLY 3.2 1.3 + - - -
964 SER 5.2 0.9 - - - +
1004 THR* 4.1 15.5 - - + +
1084 GLN* 3.2 52.9 + - + +
1094 PRO 4.0 2.9 - - - -
1104 VAL* 4.0 17.5 - - + -
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Residues in contact with ALA 72 (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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843 HIS* 5.4 5.7 - - + +
1323 TYR* 4.1 19.3 + - - +
1483 ILE* 4.2 16.6 - - + -
1513 ALA* 3.8 23.0 - - + +
1553 ASN* 5.3 5.9 + - - -
684 GLY 2.9 16.3 + - - +
694 ALA 3.1 7.3 + - - +
714 MET* 1.3 76.4 - - - +
734 GLY* 1.3 56.5 + - - +
744 LEU* 3.7 2.1 + - - +
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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
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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