Contacts of the helix formed by residues 1595 - 1611 (chain X) in PDB entry 3HM6
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 ARG1595 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1591X VAL* 3.8 12.6 - - + -
1592X PRO* 2.8 30.1 + - + +
1594X SER* 1.3 78.7 + - - +
1596X ARG* 1.3 56.0 + - - +
1597X PRO* 3.5 1.6 - - - -
1598X THR* 3.3 28.7 + - - +
1599X VAL* 2.9 36.6 + - - +
2126X ALA 3.9 3.0 + - - -
2127X ALA* 2.8 29.1 + - - +
2128X VAL 4.2 0.4 - - - -
2129X GLU* 3.3 31.9 + - - +
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Residues in contact with ARG1596 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1589X LEU* 5.1 4.9 - - + -
1591X VAL* 3.9 17.0 - - + +
1592X PRO 3.2 7.7 + - - +
1593X GLU* 3.4 15.0 + - - +
1595X ARG* 1.3 75.7 - - - +
1597X PRO* 1.3 63.1 - - + +
1599X VAL* 3.6 1.0 - - - +
1600X GLU* 2.8 75.5 + - + +
2085X ARG* 3.9 19.7 - - - +
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Residues in contact with PRO1597 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1593X GLU 3.8 9.0 - - - +
1594X SER 4.1 6.5 - - - +
1595X ARG 3.7 3.4 - - - -
1596X ARG* 1.3 95.7 - - + +
1598X THR* 1.3 54.2 + - - +
1600X GLU* 3.3 7.8 + - + +
1601X GLN* 2.7 38.7 + - - +
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Residues in contact with THR1598 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1594X SER 4.7 4.9 + - - -
1595X ARG* 3.3 35.8 + - - +
1597X PRO* 1.3 75.3 - - - +
1599X VAL* 1.3 67.9 + - - +
1601X GLN* 3.2 14.9 + - + +
1602X GLY* 2.9 18.2 + - - -
2127X ALA* 3.3 32.5 - - + +
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Residues in contact with VAL1599 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1589X LEU* 4.3 5.6 - - + -
1591X VAL* 3.5 38.8 - - + -
1595X ARG* 2.9 36.9 + - + +
1596X ARG 3.6 3.6 - - - +
1598X THR* 1.3 75.9 - - - +
1600X GLU* 1.3 57.2 + - - +
1602X GLY* 3.0 3.6 + - - -
1603X LEU* 2.8 41.2 + - + +
2089X HIS* 4.5 3.1 - - + +
2127X ALA 4.0 7.2 - - - +
2128X VAL* 3.9 33.9 - - + +
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Residues in contact with GLU1600 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1589X LEU* 4.3 15.0 - - + -
1596X ARG* 2.8 60.0 + - + +
1597X PRO* 3.8 6.7 - - + +
1599X VAL* 1.3 69.7 - - - +
1601X GLN* 1.3 60.7 + - - +
1603X LEU* 3.2 12.3 + - + +
1604X GLY* 2.9 26.0 + - - -
2085X ARG* 2.8 34.6 + - + +
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Residues in contact with GLN1601 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1597X PRO* 2.7 23.9 + - - +
1598X THR* 3.3 13.7 - - + +
1600X GLU* 1.3 71.5 - - - +
1602X GLY* 1.3 61.3 + - - +
1604X GLY* 3.3 3.7 + - - -
1605X GLN* 3.2 28.8 + - + +
2127X ALA* 5.8 2.7 - - + -
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Residues in contact with GLY1602 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1598X THR 2.9 13.4 + - - -
1599X VAL 3.0 4.6 + - - -
1601X GLN* 1.3 75.0 - - - +
1603X LEU* 1.3 58.3 + - - +
1605X GLN* 3.2 5.8 + - - -
1606X LEU* 2.9 24.1 + - - +
2124X ILE* 3.4 19.7 - - - +
2127X ALA* 4.0 13.6 - - - +
2128X VAL* 3.9 14.4 - - - -
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Residues in contact with LEU1603 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1589X LEU* 4.2 20.4 - - + -
1599X VAL* 2.8 26.1 + - + +
1600X GLU* 3.2 13.9 + - + +
1602X GLY* 1.3 71.2 - - - +
1604X GLY* 1.3 65.2 + - - +
1606X LEU* 3.3 8.1 + - + +
1607X SER 3.0 18.0 + - - -
2085X ARG* 3.6 25.6 - - + +
2088X LEU* 3.4 29.2 - - + +
2089X HIS* 3.9 38.8 - - + +
2092X TYR* 4.5 7.4 - - + -
2128X VAL* 4.4 13.7 - - + -
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Residues in contact with GLY1604 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1600X GLU 2.9 13.9 + - - -
1601X GLN* 3.3 5.1 + - - -
1602X GLY 3.3 0.2 - - - -
1603X LEU* 1.3 75.9 - - - +
1605X GLN* 1.3 56.7 + - - +
1607X SER* 3.1 11.5 - - - -
1608X ASN* 3.0 30.5 + - - +
2088X LEU* 5.2 1.3 - - - -
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Residues in contact with GLN1605 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1601X GLN* 3.2 19.0 + - + +
1602X GLY* 3.2 9.4 + - - +
1604X GLY* 1.3 73.9 - - - +
1606X LEU* 1.3 60.0 + - - +
1608X ASN* 2.6 36.6 + - - +
1609X LEU* 2.9 27.2 + - - +
2120X ARG* 5.0 5.6 + - - -
2124X ILE* 3.7 17.4 - - + +
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Residues in contact with LEU1606 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1602X GLY 2.9 12.6 + - - +
1603X LEU* 3.6 12.8 - - + +
1604X GLY 3.3 0.2 - - - -
1605X GLN* 1.3 73.7 - - - +
1607X SER* 1.3 59.7 + - - +
1609X LEU* 3.2 6.2 + - + -
1610X LEU* 2.8 44.0 + - + +
1615X PHE* 4.6 7.0 - - + -
2088X LEU* 3.6 34.1 - - + +
2091X LEU* 4.5 6.3 - - + -
2092X TYR* 4.1 15.9 - - + +
2095X ILE* 3.7 33.0 - - + -
2121X LEU* 4.8 0.2 - - + -
2124X ILE* 3.6 22.3 - - + +
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Residues in contact with SER1607 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1603X LEU 3.0 12.3 + - - -
1604X GLY* 3.1 15.9 - - - -
1606X LEU* 1.3 76.3 - - - +
1608X ASN* 1.3 61.8 + - - +
1610X LEU* 3.2 19.0 + - - +
1611X ASN* 3.6 13.0 + - - +
1644X ALA* 4.8 8.7 + - - +
1645X LEU* 5.6 0.2 - - - +
2088X LEU* 3.8 25.3 - - - +
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Residues in contact with ASN1608 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1604X GLY 3.0 17.1 + - - +
1605X GLN* 2.6 36.5 + - - +
1606X LEU 3.3 0.2 - - - -
1607X SER* 1.3 75.8 - - - +
1609X LEU* 1.3 65.5 + - - +
1611X ASN* 3.0 30.0 + - - +
1612X SER 4.0 1.2 + - - -
2120X ARG* 4.3 13.8 + - - +
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Residues in contact with LEU1609 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1605X GLN 2.9 17.0 + - - +
1606X LEU* 3.2 10.0 + - + +
1608X ASN* 1.3 72.6 - - - +
1610X LEU* 1.3 58.4 + - - +
1612X SER* 2.9 28.4 + - - -
1615X PHE* 3.7 43.8 - - + -
2117X LEU* 4.1 15.9 - - + +
2120X ARG* 3.2 47.5 - - + +
2121X LEU* 4.0 20.9 - - + +
2124X ILE* 3.4 24.7 - - + -
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Residues in contact with LEU1610 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1606X LEU* 2.8 24.8 + - + +
1607X SER* 3.5 9.9 - - - +
1608X ASN 3.2 0.6 - - - -
1609X LEU* 1.3 75.4 - - - +
1611X ASN* 1.3 50.0 + - - +
1612X SER 3.3 3.5 + - - +
1615X PHE* 3.9 20.4 - - + -
1616X LEU* 3.7 21.4 - - + +
1619X PHE* 4.4 7.9 - - + -
1641X LEU* 3.7 24.0 - - + -
1644X ALA* 4.2 11.0 - - + -
1645X LEU* 4.3 13.6 - - + +
1651X TYR* 2.6 30.2 + - - -
2088X LEU* 3.7 29.8 - - + -
2091X LEU* 4.0 17.5 - - + -
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Residues in contact with ASN1611 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1607X SER 3.8 14.5 + - - +
1608X ASN* 3.0 21.7 + - - +
1609X LEU 2.9 0.4 + - - -
1610X LEU* 1.3 74.2 - - - +
1612X SER* 1.3 62.3 + - - +
1613X LYS 3.5 2.9 + - - -
1645X LEU* 4.0 12.8 - - - +
1648X LYS* 3.6 41.6 + - - +
1651X TYR* 3.3 18.1 + - - -
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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
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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