Contacts of the helix formed by residues 985 - 998 (chain A) in PDB entry 3H0G
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 LEU 985 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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917A MET* 4.0 5.6 - - + -
920A SER* 5.5 4.3 - - - +
922A GLU* 3.6 27.8 - - - +
929A ASP* 5.6 6.1 - - - +
984A LEU* 1.3 88.1 - - - +
986A PRO* 1.3 70.9 - - + +
987A SER* 2.8 42.1 + - - +
988A ASP* 2.6 52.4 + - - +
989A ILE* 3.5 6.4 + - - +
1042A LYS* 5.2 2.9 - - - +
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Residues in contact with PRO 986 (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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913A LEU* 6.2 1.8 - - + -
917A MET* 3.3 34.5 - - + -
929A ASP* 6.0 7.9 - - + -
932A ASP* 4.9 1.2 - - - +
933A GLU* 3.7 22.7 - - - +
985A LEU* 1.3 90.1 - - + +
987A SER* 1.3 54.7 + - - +
988A ASP 3.2 0.9 - - - -
989A ILE* 2.9 29.9 - - + +
990A ILE* 3.3 13.7 - - - +
1031A VAL* 4.1 8.3 - - + -
1035A ILE* 4.5 14.3 - - + -
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Residues in contact with SER 987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929A ASP* 4.9 10.8 + - - -
932A ASP* 4.0 12.5 + - - -
985A LEU* 2.8 22.7 + - - +
986A PRO* 1.3 78.1 - - - +
988A ASP* 1.3 64.4 + - - +
990A ILE* 3.9 10.3 - - - +
991A ASN* 3.0 29.8 + - - +
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Residues in contact with ASP 988 (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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984A LEU* 4.5 7.5 - - + +
985A LEU* 2.6 42.9 + - - +
987A SER* 1.3 80.6 - - - +
989A ILE* 1.3 56.0 + - + +
990A ILE 3.0 1.6 - - - -
991A ASN* 2.9 7.8 + - - +
992A GLY* 2.5 36.4 + - - -
1042A LYS* 4.2 19.1 + - - +
1045A PHE* 4.9 4.7 - - + -
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Residues in contact with ILE 989 (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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984A LEU* 3.7 30.1 - - + -
985A LEU 4.0 8.7 - - - +
986A PRO* 2.9 38.1 - - + +
988A ASP* 1.3 76.5 - - + +
990A ILE* 1.3 80.4 + - + +
992A GLY* 3.3 7.1 + - - -
993A LEU* 3.3 20.6 + - - +
1029A PHE 4.1 18.2 - - - +
1031A VAL* 3.7 23.3 - - + -
1034A VAL* 4.9 10.1 - - + -
1035A ILE* 6.2 4.3 - - + -
1045A PHE* 3.6 29.5 - - + -
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Residues in contact with ILE 990 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A ASP* 2.8 42.6 - - + +
933A GLU* 5.6 1.1 - - - +
936A THR* 4.6 13.9 - - - +
986A PRO 3.3 14.6 - - - +
987A SER* 3.9 9.9 - - - +
989A ILE* 1.3 98.2 - - + +
991A ASN* 1.3 76.3 + - - +
993A LEU* 3.7 5.5 + - + +
994A ASN* 3.0 32.6 + - - +
1030A ALA* 6.5 0.2 - - - -
1031A VAL* 3.7 16.8 - - + -
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Residues in contact with ASN 991 (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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987A SER* 3.0 23.9 + - - +
988A ASP* 2.9 8.5 + - - +
990A ILE* 1.3 87.4 - - - +
992A GLY* 1.3 67.6 + - - +
993A LEU 3.1 0.2 + - - -
994A ASN* 3.2 7.3 + - - +
995A GLU* 3.1 44.1 + - - +
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Residues in contact with GLY 992 (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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988A ASP 2.5 20.0 + - - -
989A ILE 3.6 4.0 - - - -
990A ILE 3.3 0.4 - - - -
991A ASN* 1.3 73.2 - - - +
993A LEU* 1.3 62.8 + - - +
995A GLU* 3.6 4.0 + - - +
996A LEU* 3.2 19.6 + - - +
1045A PHE* 4.1 14.8 - - - -
1049A MET* 3.2 15.9 - - - +
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Residues in contact with LEU 993 (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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989A ILE 3.3 13.8 + - - +
990A ILE* 4.0 5.4 - - - +
991A ASN 3.2 0.6 - - - -
992A GLY* 1.3 70.2 - - - +
994A ASN* 1.3 66.2 + - - +
995A GLU 2.6 5.8 + - - -
996A LEU 2.3 27.9 + - - -
997A ILE* 2.7 24.9 + - + -
1025A LEU* 3.0 44.6 - - + +
1026A ARG* 4.3 16.2 - - + -
1029A PHE* 4.2 21.8 - - + +
1030A ALA* 5.7 0.9 - - - -
1045A PHE* 5.5 0.2 - - + -
1049A MET* 3.8 24.9 - - + +
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Residues in contact with ASN 994 (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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935A TYR* 6.3 0.8 - - - -
990A ILE* 3.0 21.5 + - - +
991A ASN* 3.2 8.2 + - - +
993A LEU* 1.3 80.5 - - - +
995A GLU* 1.3 60.3 + - + +
997A ILE* 4.0 15.7 - - - +
998A ALA* 3.4 22.3 + - - +
1026A ARG* 5.9 1.4 + - - -
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Residues in contact with GLU 995 (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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991A ASN* 3.1 31.2 + - - +
992A GLY* 4.0 4.6 - - - +
993A LEU 2.6 4.9 + - - -
994A ASN* 1.3 80.0 - - + +
996A LEU* 1.3 69.5 + - + +
997A ILE 3.6 0.2 - - - -
998A ALA* 4.2 4.9 - - - +
999A LYS* 3.7 13.3 + - - +
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Residues in contact with LEU 996 (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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992A GLY* 3.2 7.5 + - - +
993A LEU 2.3 20.5 + - - -
995A GLU* 1.3 82.1 - - + +
997A ILE* 1.3 60.7 + - - +
999A LYS* 3.8 32.3 - - + +
1000A LEU* 3.1 19.3 - - - +
1025A LEU* 5.1 2.8 - - - +
1046A GLU* 5.8 4.3 - - - +
1049A MET* 3.3 60.7 - - + +
1052A VAL* 5.9 1.4 - - - +
1053A GLU* 4.4 11.3 + - + +
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Residues in contact with ILE 997 (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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993A LEU* 2.7 37.9 + - + +
994A ASN* 4.0 17.0 - - + +
996A LEU* 1.3 75.9 - - - +
998A ALA* 1.3 66.3 + - + +
999A LYS 2.9 4.7 - - - -
1000A LEU* 2.9 36.6 + - + +
1014A GLN* 5.3 2.3 - - - +
1022A GLN* 3.5 19.5 - - + +
1025A LEU* 4.2 22.9 - - + -
1026A ARG* 3.4 33.2 - - + +
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Residues in contact with ALA 998 (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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994A ASN 3.4 18.1 + - - +
995A GLU* 4.2 5.2 - - - +
996A LEU 4.1 0.2 - - - +
997A ILE* 1.3 85.5 - - + +
999A LYS* 1.3 55.9 - - - -
1000A LEU 3.4 0.2 - - - -
1001A THR* 4.8 9.8 - - - +
1014A GLN* 6.3 0.7 - - - +
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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