Contacts of the helix formed by residues 1567 - 1577 (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 ASP1567 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16X UNX 3.4 14.6 - - - -
1565X PHE 3.6 3.6 + - - +
1566X LEU* 1.3 77.3 - - - +
1568X TYR* 1.3 66.1 + - - +
1569X LYS* 3.2 2.2 - - + +
1570X VAL* 3.1 25.3 + - + +
1571X TYR* 3.1 8.3 + - - +
1696X TYR* 3.9 2.0 - - - -
1700X ARG* 4.8 6.8 + - - +
2079X SER* 5.5 3.0 + - - -
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Residues in contact with TYR1568 (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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12X UNX 4.3 9.2 - - - -
16X UNX 3.3 6.9 - - - -
1567X ASP* 1.3 71.7 - - - +
1569X LYS* 1.3 59.4 + - - +
1571X TYR* 3.4 13.7 + + - +
1572X ALA* 2.9 44.2 + - + +
1576X PHE* 4.4 0.5 - - - -
1646X HIS* 2.7 40.9 + + - -
1693X ILE* 3.2 25.9 - - + +
1696X TYR* 3.3 60.8 + + + -
2077X ASN 5.6 0.7 - - - +
2078X TYR* 3.6 36.8 - + + -
2082X LEU* 4.5 4.7 - - + -
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Residues in contact with LYS1569 (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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16X UNX 3.0 17.7 - - - -
1567X ASP* 5.2 0.9 - - + -
1568X TYR* 1.3 78.6 - - - +
1570X VAL* 1.3 77.3 + - + +
1572X ALA* 3.8 1.6 - - - +
1573X GLU* 3.1 57.6 + - - +
2078X TYR* 4.8 2.5 - - + -
2079X SER 3.9 5.8 - - - +
2080X GLY* 3.9 8.1 - - - -
2081X ASP 3.8 36.1 - - - +
2082X LEU* 3.9 20.2 - - + +
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Residues in contact with VAL1570 (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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1566X LEU* 4.0 17.5 - - + -
1567X ASP* 3.1 18.1 + - + +
1569X LYS* 1.3 95.2 - - + +
1571X TYR* 1.3 66.9 + - - +
1572X ALA 3.2 0.2 + - - -
1573X GLU* 3.3 12.7 + - - +
1574X ARG* 2.9 65.7 + - + +
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Residues in contact with TYR1571 (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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1566X LEU* 4.0 10.0 - - + +
1567X ASP 3.1 11.8 + - - +
1568X TYR* 3.5 17.0 - + - +
1570X VAL* 1.3 76.1 - - - +
1572X ALA* 1.3 61.8 + - - +
1574X ARG* 3.4 2.8 + - - +
1575X ILE* 3.0 51.7 + - + +
1576X PHE* 6.5 0.2 - + - -
1692X SER* 2.6 34.9 + - - -
1696X TYR* 3.5 46.7 - + + -
1699X VAL* 4.7 7.8 - - + +
1985X PHE* 3.4 23.2 - - - -
1989X ILE* 4.7 2.7 - - + -
1995X PHE 3.2 29.1 - - - +
1996X VAL* 4.2 22.2 - - + -
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Residues in contact with ALA1572 (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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1568X TYR* 2.9 35.8 + - + +
1569X LYS 3.8 3.6 - - - +
1571X TYR* 1.3 77.0 - - + +
1573X GLU* 1.3 57.2 + - - +
1575X ILE* 4.8 1.1 - - - -
1576X PHE* 2.8 65.1 + - + -
1692X SER* 6.5 0.2 - - - -
2082X LEU* 3.9 17.9 - - + -
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Residues in contact with GLU1573 (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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1569X LYS* 3.1 56.3 + - + +
1570X VAL* 3.6 15.9 - - - +
1572X ALA* 1.3 76.8 - - - +
1574X ARG* 1.3 60.3 + - + +
1576X PHE* 4.6 1.8 - - - -
1577X PHE* 2.9 45.2 + - + +
1583X SER* 3.9 32.1 + - - +
2081X ASP 4.7 2.9 - - - +
2082X LEU* 4.9 14.9 - - + +
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Residues in contact with ARG1574 (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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1566X LEU* 3.7 20.5 - - - +
1570X VAL* 2.9 38.6 + - + +
1571X TYR 3.7 3.8 - - - +
1573X GLU* 1.3 79.0 - - + +
1575X ILE* 1.3 60.6 + - - +
1577X PHE 4.6 3.6 - - - -
1578X PRO* 3.3 24.3 - - - +
1795X THR* 5.2 4.6 + - - -
1994X GLN* 2.8 48.1 + - - +
1995X PHE* 3.5 24.3 - - + -
1997X PHE 3.9 8.5 + - - -
1998X ASP* 4.4 12.9 + - - -
1999X VAL 4.7 4.6 + - - -
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Residues in contact with ILE1575 (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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1571X TYR* 3.0 56.4 + - + +
1572X ALA* 4.1 2.5 - - - +
1574X ARG* 1.3 74.2 - - - +
1576X PHE* 1.3 64.8 + - + +
1578X PRO* 3.4 7.4 - - - +
1685X LYS* 2.8 22.7 + - - -
1688X THR* 4.4 5.8 - - + -
1689X ASN* 4.4 9.6 - - - +
1692X SER* 3.4 31.9 - - - +
1985X PHE* 4.6 0.7 - - + -
1988X ASN* 4.1 16.1 + - - +
1989X ILE* 4.1 15.7 - - + -
1995X PHE* 3.8 26.9 - - + -
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Residues in contact with PHE1576 (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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1568X TYR* 4.4 1.8 - - - -
1571X TYR* 6.5 0.4 - + - -
1572X ALA* 2.8 48.1 + - + +
1573X GLU* 4.7 0.9 - - - -
1575X ILE* 1.3 76.4 - - + +
1577X PHE* 1.3 71.9 + + + +
1578X PRO* 3.4 6.0 - - - +
1635X ALA 4.7 1.0 - - - +
1636X TYR* 5.7 0.5 - - - -
1639X SER* 2.6 35.0 + - - +
1642X THR* 3.4 27.8 - - + -
1643X VAL* 3.8 25.1 - - + -
1646X HIS* 4.5 0.7 - + - -
1685X LYS* 3.5 5.4 - - - -
1689X ASN* 3.2 41.3 - - + -
1692X SER* 4.9 7.0 - - - -
1693X ILE* 4.0 15.7 - - + -
2082X LEU* 4.5 11.4 - - + -
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Residues in contact with PHE1577 (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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2X UNX 3.2 11.9 - - - -
1573X GLU* 2.9 24.6 + - + +
1574X ARG* 3.7 6.0 - - - +
1576X PHE* 1.3 90.8 - + + +
1578X PRO* 1.4 65.2 - - - +
1579X GLY 3.3 3.0 + - - -
1580X HIS* 3.5 13.8 + - + +
1583X SER* 4.1 8.9 - - - -
1584X PRO* 3.7 26.2 - - + -
1585X LEU* 3.7 36.1 - - + -
1636X TYR* 3.7 38.4 - + - -
1639X SER* 3.5 35.4 - - - -
1640X LEU* 4.3 3.1 - - + -
1643X VAL* 4.3 6.1 - - + -
2082X LEU 5.2 1.1 - - - -
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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