Contacts of the helix formed by residues 927 - 934 (chain A) in PDB entry 5FLM
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 GLU 927 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924A TYR 3.8 4.1 + - - +
925A THR 3.4 6.4 - - - +
926A ASN* 1.3 78.8 - - - +
928A ARG* 1.3 59.3 + - + +
929A ALA 3.6 0.2 - - - -
930A LEU* 3.9 22.3 - - - +
931A ARG* 3.0 55.3 + - + +
939A VAL* 4.5 1.1 - - + +
943A LEU* 3.6 27.8 - - + +
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Residues in contact with ARG 928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926A ASN* 2.9 14.2 + - + +
927A GLU* 1.3 77.6 - - + +
929A ALA* 1.3 60.5 + - - +
930A LEU 3.1 1.3 - - - -
931A ARG* 3.2 8.9 + - - +
932A ARG* 2.9 27.5 + - - +
106H THR* 2.8 59.6 + - + +
107H GLU* 4.9 4.8 - - - +
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Residues in contact with ALA 929 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923A ASP 5.8 2.9 - - - +
926A ASN* 4.2 19.3 - - + +
928A ARG* 1.3 78.9 - - - +
930A LEU* 1.3 53.5 + - + +
932A ARG* 3.7 7.0 - - - -
933A THR* 2.7 44.3 + - + +
1052A ARG* 6.2 2.2 - - - +
105H SER* 3.4 25.8 - - - +
106H THR* 3.3 10.4 - - + +
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Residues in contact with LEU 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922A PHE* 4.1 29.2 - - + -
923A ASP 4.2 7.4 - - - +
924A TYR* 3.2 39.5 - - + +
926A ASN* 5.9 0.4 - - + -
927A GLU* 3.9 14.1 - - - +
928A ARG 3.1 0.6 - - - -
929A ALA* 1.3 77.7 - - + +
931A ARG* 1.3 53.4 + - - +
933A THR* 4.0 5.4 - - - +
934A LEU* 2.7 52.1 + - + +
939A VAL* 3.5 26.9 - - + +
942A VAL* 5.1 5.4 - - + -
943A LEU* 3.7 19.1 - - + -
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Residues in contact with ARG 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927A GLU* 3.0 41.9 + - - +
928A ARG* 3.2 9.1 + - - +
930A LEU* 1.3 76.8 - - - +
932A ARG* 1.3 62.0 + - - +
934A LEU 3.0 15.9 - - - +
936A GLU* 3.2 41.4 + - - +
939A VAL* 3.2 34.0 - - + +
940A LYS* 4.3 20.6 - - - +
943A LEU* 6.0 0.6 - - - +
1001A PRO* 4.3 5.0 - - - +
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Residues in contact with ARG 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928A ARG 2.9 15.5 + - - +
929A ALA* 3.5 6.5 + - - +
930A LEU 3.2 0.2 - - - -
931A ARG* 1.3 79.6 - - - +
933A THR* 1.3 69.1 + - + +
999A ARG* 3.7 32.5 + - - +
1000A LEU 4.8 1.4 - - - -
1001A PRO* 3.5 24.8 - - - +
1059A ARG* 5.1 4.5 + - - +
103H GLU* 2.6 32.3 + - - -
105H SER 3.4 25.6 + - - +
106H THR 4.2 12.8 - - - +
107H GLU 4.6 3.6 + - - -
108H ALA* 5.0 14.0 - - - +
109H ALA 5.3 1.0 - - - +
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Residues in contact with THR 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929A ALA* 2.7 31.5 + - + +
930A LEU* 4.0 6.8 + - - +
932A ARG* 1.3 80.0 - - + +
934A LEU* 1.3 66.9 + - - +
1001A PRO* 3.4 2.3 - - - +
1002A SER* 2.9 29.0 + - - -
1055A ALA* 3.3 30.0 + - - +
1056A GLU* 5.2 5.8 - - + -
1059A ARG* 3.5 29.9 + - - +
105H SER* 5.6 5.4 - - - +
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Residues in contact with LEU 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922A PHE* 5.4 4.0 - - + -
930A LEU* 2.7 41.5 + - + +
931A ARG* 3.0 14.4 - - - +
933A THR* 1.3 78.6 + - - +
935A GLN* 1.3 78.0 + - - +
938A LEU* 3.9 24.0 - - + +
939A VAL* 4.2 5.4 - - + +
942A VAL* 3.9 28.9 - - + -
1001A PRO* 4.0 2.2 - - - +
1002A SER* 3.7 10.5 - - - +
1004A LEU 3.2 27.1 - - - +
1006A PRO* 4.3 9.9 - - + -
1055A ALA* 5.8 8.1 - - + -
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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