Contacts of the helix formed by residues 152 - 171 (chain 4) in PDB entry 5LN3
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 152 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104 PRO* 5.6 0.4 - - - +
114 ASP* 4.5 1.8 - - - -
1514 ILE* 1.4 77.8 - - - +
1534 ARG* 1.4 65.9 + - - +
1544 GLU* 3.3 21.1 - - - -
1554 ARG* 3.7 21.0 - - - +
1564 ALA* 3.7 5.4 + - - +
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Residues in contact with ARG 153 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114 ASP* 3.8 41.7 + - - +
124 TYR* 3.0 51.6 + - + +
1524 SER* 1.4 74.5 - - - +
1544 GLU* 1.4 82.0 + - - +
1564 ALA* 3.4 11.1 + - - +
1574 VAL* 3.8 2.6 + - - +
1844 ASP* 6.0 0.6 + - - -
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Residues in contact with GLU 154 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524 SER* 3.3 16.5 - - - -
1534 ARG* 1.4 107.6 + - - +
1554 ARG* 1.4 62.0 + - + +
1564 ALA 3.4 0.3 + - - -
1574 VAL* 3.4 15.2 + - - +
1584 GLU* 3.6 18.4 + - - +
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Residues in contact with ARG 155 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1464 TYR* 3.5 43.6 + - - +
1514 ILE* 3.5 33.7 - - + +
1524 SER* 3.7 25.8 - - - +
1544 GLU* 1.4 76.3 - - + +
1564 ALA* 1.4 61.5 + - - +
1584 GLU* 3.4 22.8 + - - +
1594 LEU* 3.2 26.3 + - - +
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Residues in contact with ALA 156 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74 ILE* 4.7 20.0 - - + -
124 TYR* 4.0 10.3 - - + -
144 LEU* 3.6 22.9 - - + -
1514 ILE* 4.9 4.0 - - + +
1524 SER 3.7 7.1 + - - +
1534 ARG 3.4 11.9 + - - +
1544 GLU 3.4 0.8 - - - -
1554 ARG* 1.4 76.6 - - - +
1574 VAL* 1.3 63.3 + - - +
1594 LEU* 3.1 8.7 + - - +
1604 LEU* 2.9 27.9 + - - +
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Residues in contact with VAL 157 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124 TYR* 3.2 26.5 - - + +
144 LEU* 4.5 7.9 - - + -
1534 ARG* 3.9 3.8 - - + +
1544 GLU* 3.4 8.9 + - - +
1554 ARG 3.3 0.8 - - - -
1564 ALA* 1.3 76.4 - - - +
1584 GLU* 1.4 63.8 + - - +
1604 LEU* 3.7 7.1 + - - +
1614 ARG* 3.4 19.6 + - - +
1824 ILE* 6.4 0.7 - - + -
1914 LEU* 4.3 30.7 - - + +
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Residues in contact with GLU 158 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544 GLU 3.6 16.0 - - - +
1554 ARG* 3.5 24.2 - - - +
1574 VAL* 1.4 79.8 - - - +
1594 LEU* 1.4 64.3 + - - +
1614 ARG* 3.2 17.4 + - - +
1624 LYS* 3.3 17.1 + - + +
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Residues in contact with LEU 159 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74 ILE* 4.5 10.1 - - + -
1424 ILE* 3.5 23.6 - - + -
1434 LEU* 3.8 33.9 - - + -
1464 TYR* 3.9 29.4 - - + -
1474 TYR* 4.1 19.7 - - + +
1514 ILE* 5.4 4.3 - - + -
1554 ARG* 3.2 14.9 + - - +
1564 ALA* 3.1 10.5 + - - +
1584 GLU* 1.4 77.9 - - - +
1604 LEU* 1.3 66.5 + - + +
1624 LYS* 3.1 23.0 + - - +
1634 CYS* 3.6 10.1 + - - -
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Residues in contact with LEU 160 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54 ILE* 6.0 4.9 - - + -
74 ILE* 4.0 19.7 - - + -
144 LEU* 3.8 26.7 - - + +
154 VAL 5.6 0.4 - - - -
164 ALA* 4.7 13.0 - - + +
1434 LEU* 6.0 1.3 - - + -
1564 ALA* 2.9 20.9 + - + +
1574 VAL 3.8 5.6 - - - +
1594 LEU* 1.3 82.0 - - + +
1614 ARG* 1.4 62.4 + - - +
1634 CYS* 3.2 31.3 + - + +
1644 LEU* 3.7 13.0 + - + +
1784 PHE* 5.7 3.1 - - + -
1804 VAL* 4.1 28.7 - - + -
1914 LEU* 4.4 15.5 - - + -
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Residues in contact with ARG 161 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1574 VAL 3.4 11.0 + - - +
1584 GLU* 3.2 14.5 + - - +
1604 LEU* 1.4 76.5 - - - +
1624 LYS* 1.3 61.7 + - + +
1634 CYS 3.3 0.5 + - - -
1644 LEU* 3.4 28.9 + - - +
1654 GLU* 2.8 39.8 + - - +
1914 LEU* 6.3 0.8 - - - +
1924 ASP 4.1 17.0 + - - -
1944 ILE* 3.8 37.0 - - - +
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Residues in contact with LYS 162 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1424 ILE* 4.4 16.8 - - + -
1464 TYR* 3.0 44.2 + - + +
1584 GLU 3.3 14.2 + - - +
1594 LEU* 3.1 14.1 + - - +
1614 ARG* 1.3 77.8 - - - +
1634 CYS* 1.4 56.2 + - - +
1654 GLU* 3.2 14.9 + - + +
1664 GLU* 3.1 28.3 + - + +
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Residues in contact with CYS 163 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54 ILE* 5.8 3.6 - - - -
1384 LEU* 6.0 0.3 - - - +
1394 THR* 3.8 34.7 - - + +
1424 ILE* 3.8 19.7 - - - -
1434 LEU* 5.7 3.6 - - - -
1594 LEU* 4.0 16.8 - - - -
1604 LEU* 3.2 25.5 + - + +
1614 ARG 3.2 0.4 - - - -
1624 LYS* 1.4 59.9 - - - +
1644 LEU* 1.3 65.6 + - + +
1664 GLU* 3.1 6.1 + - - +
1674 LEU* 3.0 23.1 + - - +
1784 PHE* 4.8 11.4 - - + -
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Residues in contact with LEU 164 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1604 LEU* 3.8 14.8 - - + +
1614 ARG* 3.4 32.3 + - - +
1624 LYS 3.4 0.2 - - - -
1634 CYS* 1.3 78.1 - - + +
1654 GLU* 1.3 58.1 + - - +
1674 LEU* 3.4 8.0 + - + +
1684 GLN* 2.9 43.4 + - - +
1774 THR* 3.9 29.0 - - + +
1784 PHE* 4.0 29.6 - - + +
1804 VAL* 5.4 2.7 - - + -
1934 ASN* 3.7 26.5 - - + +
1944 ILE* 4.5 16.2 - - + +
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Residues in contact with GLU 165 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1614 ARG* 2.8 44.8 - - - +
1624 LYS* 3.2 16.7 + - + +
1644 LEU* 1.3 78.3 - - - +
1664 GLU* 1.3 50.1 + - + +
1684 GLN* 3.4 19.4 + - - +
1694 LYS* 2.9 58.6 + - + +
1944 ILE* 4.5 10.5 - - - +
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Residues in contact with GLU 166 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1384 LEU* 4.4 21.6 - - + +
1394 THR* 6.5 0.2 - - + -
1424 ILE* 4.2 22.2 - - + -
1624 LYS* 3.1 13.6 + - + +
1634 CYS* 3.4 10.1 - - - +
1654 GLU* 1.3 70.4 - - - +
1674 LEU* 1.3 57.3 + - - +
1694 LYS* 3.0 17.6 + - + +
1704 ARG* 2.8 43.5 + - - +
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Residues in contact with LEU 167 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1344 TYR 6.4 0.2 - - - -
1354 GLY* 5.3 4.9 - - - -
1384 LEU* 4.1 18.1 - - + +
1394 THR* 6.6 0.2 - - + -
1634 CYS 3.0 12.2 + - - +
1644 LEU* 3.6 9.6 - - + +
1664 GLU* 1.3 72.9 - - - +
1684 GLN* 1.4 62.9 + - + +
1714 PHE* 3.3 22.2 + - - -
1724 ILE* 3.2 38.9 + - + +
1734 LEU* 5.3 9.6 - - + -
1754 LEU 5.8 1.3 - - - +
1774 THR* 4.0 27.6 - - + +
1784 PHE* 3.4 42.6 - - + -
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Residues in contact with GLN 168 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1644 LEU* 2.9 36.7 + - - +
1654 GLU* 3.4 27.1 + - - +
1674 LEU* 1.4 76.5 - - + +
1694 LYS* 1.3 66.3 + - + +
1714 PHE* 3.9 17.8 + - - +
1774 THR* 4.5 16.0 - - + +
1944 ILE* 4.3 15.1 - - - +
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Residues in contact with LYS 169 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1654 GLU* 2.9 44.0 + - + +
1664 GLU* 3.0 21.0 + - + +
1684 GLN* 1.3 78.3 - - + +
1704 ARG* 1.3 65.3 + - - +
1714 PHE* 4.1 2.9 - - - +
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Residues in contact with ARG 170 (chain 4).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1384 LEU* 4.1 22.9 - - + -
1664 GLU* 2.8 22.5 + - - +
1694 LYS* 1.3 74.4 - - - +
1714 PHE* 1.3 87.2 + - - +
1724 ILE* 4.0 23.8 - - - +
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Residues in contact with PHE 171 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1674 LEU 3.3 12.2 + - - -
1684 GLN* 4.1 13.2 - - - +
1694 LYS 3.1 6.3 - - - +
1704 ARG* 1.3 110.1 + - - +
1724 ILE* 1.4 67.5 - - - +
1734 LEU 3.7 23.1 - - - -
1744 ASN* 4.9 9.4 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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