Contacts of the helix formed by residues 984 - 998 (chain A) in PDB entry 3UGM
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 GLN 984 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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981A GLY 3.3 11.9 - - - +
982A GLY 2.7 7.7 + - - -
983A LYS* 1.3 103.1 - - - +
985A ALA* 1.3 62.8 + - - +
986A LEU 3.2 1.8 - - - -
987A GLU* 3.6 9.5 + - - +
988A THR* 3.2 28.2 + - - -
991A ARG* 6.3 0.2 - - - +
1016A LYS* 3.3 34.3 - - + +
20B A 3.7 29.5 + - - +
21B C 3.9 12.6 - - - +
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Residues in contact with ALA 985 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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976A ILE* 3.9 8.6 - - + +
981A GLY* 3.6 18.2 + - - -
982A GLY 3.3 3.1 + - - +
984A GLN* 1.3 78.6 - - - +
986A LEU* 1.3 64.4 + - - +
988A THR* 4.0 0.4 - - - -
989A VAL* 3.0 26.7 + - - +
1011A ALA* 3.6 25.1 - - - +
1015A GLY* 3.7 17.7 - - - -
1016A LYS* 3.7 12.3 - - - +
1019A LEU* 4.0 2.8 - - - +
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Residues in contact with LEU 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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951A ALA 4.7 1.3 - - - +
954A THR* 3.6 32.5 - - + +
955A VAL* 3.8 28.7 - - + -
958A LEU* 5.0 7.2 - - + +
962A LEU* 6.2 1.4 - - + +
973A VAL* 3.8 22.2 - - + +
976A ILE* 3.5 36.8 - - + -
977A ALA* 3.9 8.1 - - + +
982A GLY 3.2 16.6 + - - +
984A GLN 3.2 0.2 - - - -
985A ALA* 1.3 76.5 - - - +
987A GLU* 1.3 68.0 + - - +
989A VAL* 2.8 20.4 + - + +
990A GLN* 3.1 10.6 + - - +
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Residues in contact with GLU 987 (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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954A THR* 4.1 0.7 - - + -
957A ARG* 2.6 24.6 + - - +
958A LEU* 3.8 26.0 - - + +
983A LYS* 3.5 37.0 + - - +
984A GLN* 3.6 13.9 + - - +
985A ALA 3.5 0.4 - - - -
986A LEU* 1.3 80.6 - - - +
988A THR* 1.3 63.3 + - - +
990A GLN* 3.2 11.4 + - - +
991A ARG* 3.3 20.7 + - - +
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Residues in contact with THR 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 GLN 3.2 12.6 + - - -
985A ALA 4.2 2.5 - - - -
987A GLU* 1.3 78.1 - - - +
989A VAL* 1.3 57.5 + - - +
991A ARG* 2.6 36.7 + - - +
992A LEU* 2.9 47.3 + - + +
1016A LYS* 3.4 22.6 - - - +
1019A LEU* 3.5 23.8 - - + -
1020A GLU* 4.0 12.5 + - + -
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Residues in contact with VAL 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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962A LEU* 4.7 14.8 - - + -
968A LEU* 4.8 7.4 - - + -
976A ILE* 4.3 19.3 - - + -
985A ALA 3.0 15.3 + - - +
986A LEU* 2.8 17.4 + - + +
988A THR* 1.3 72.0 - - - +
990A GLN* 1.3 58.6 + - - +
992A LEU* 3.9 1.6 - - - -
993A LEU* 3.1 28.8 + - + +
1007A VAL* 3.7 23.1 - - + +
1011A ALA* 3.5 18.8 - - + -
1019A LEU* 3.3 24.2 - - + -
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Residues in contact with GLN 990 (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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958A LEU* 5.3 11.0 - - + -
961A VAL* 3.9 25.1 + - + +
962A LEU* 3.7 32.5 - - + +
965A ASP* 4.0 20.4 + - - +
966A HIS* 4.1 4.6 - - - -
986A LEU 3.1 9.2 + - - +
987A GLU* 3.2 7.6 + - - +
989A VAL* 1.3 75.3 - - - +
991A ARG* 1.3 55.7 + - - +
992A LEU 2.6 16.5 + - - -
993A LEU* 3.1 25.6 + - - +
994A PRO* 3.2 14.6 - - - +
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Residues in contact with ARG 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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984A GLN* 5.3 0.4 + - - +
987A GLU* 3.3 15.9 + - - +
988A THR* 2.6 42.2 + - - +
990A GLN* 1.3 78.2 - - - +
992A LEU* 1.3 74.1 + - + +
994A PRO* 4.7 8.7 - - - +
995A VAL* 5.1 3.6 - - - +
1016A LYS* 5.0 6.5 - - - +
1020A GLU* 3.9 20.2 + - - -
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Residues in contact with LEU 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 THR* 2.9 22.5 + - + +
989A VAL* 4.0 2.9 - - + +
990A GLN 2.6 7.3 + - - -
991A ARG* 1.3 97.9 - - + +
993A LEU* 1.3 67.9 + - - +
994A PRO 3.2 2.0 - - - -
995A VAL* 3.9 15.9 - - + +
996A LEU* 3.1 34.2 + - + +
1007A VAL* 5.5 3.0 - - + +
1019A LEU* 4.6 5.2 - - + -
1020A GLU* 3.4 45.5 - - + +
1023A GLN* 3.8 26.5 - - + +
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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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962A LEU* 4.6 11.2 - - + -
966A HIS* 2.5 52.0 - - + +
968A LEU* 4.8 7.9 - - + -
989A VAL* 3.1 18.5 + - + +
990A GLN* 3.1 13.1 + - - +
992A LEU* 1.3 79.7 - - - +
994A PRO* 1.4 76.5 - - + +
997A CYS* 3.3 33.8 + - - +
1004A LEU* 3.7 21.5 - - + -
1007A VAL* 4.0 25.4 - - + -
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Residues in contact with PRO 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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966A HIS* 3.7 27.4 - - + +
990A GLN* 3.2 19.5 - - - +
991A ARG* 4.7 6.1 - - - +
992A LEU 4.6 1.3 - - - -
993A LEU* 1.4 97.1 - - + +
995A VAL* 1.3 64.9 + - + +
997A CYS* 4.6 0.3 - - - +
998A GLN* 3.1 35.9 + - + +
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Residues in contact with VAL 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 ARG 5.1 2.7 - - - +
992A LEU* 3.4 23.6 + - + +
994A PRO* 1.3 86.1 - - + +
996A LEU* 1.3 53.1 + - - +
998A GLN* 4.2 1.6 - - - +
999A ASP* 2.7 56.5 + - + +
1000A HIS* 2.8 19.4 + - + +
1023A GLN* 4.3 24.2 - - + +
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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 LEU* 3.1 25.9 + - + +
993A LEU 4.6 0.2 - - - +
995A VAL* 1.3 78.4 - - - +
997A CYS* 1.3 52.9 + - - +
1000A HIS* 3.5 23.5 - - + +
1001A GLY 2.9 10.9 + - - -
1002A LEU* 2.8 55.8 + - + +
1007A VAL* 4.6 9.6 - - + -
1010A ILE* 6.5 0.2 - - + -
1019A LEU* 4.2 28.3 - - + +
1022A VAL* 4.6 6.3 - - + -
1023A GLN* 3.3 47.3 - - + +
1026A LEU* 5.5 0.7 - - + -
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Residues in contact with CYS 997 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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966A HIS* 6.4 1.1 - - + +
993A LEU* 3.3 35.6 + - + +
994A PRO 4.6 0.2 - - - +
996A LEU* 1.3 79.5 - - - +
998A GLN* 1.3 62.0 + - + +
1001A GLY* 3.5 13.9 - - - -
1002A LEU* 3.4 31.3 + - - +
1003A THR 4.4 1.1 - - - -
1004A LEU* 4.2 20.0 - - - -
1007A VAL* 5.2 4.7 - - - -
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Residues in contact with GLN 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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966A HIS* 6.6 0.2 - - + -
994A PRO* 3.1 21.2 + - + +
995A VAL* 4.2 2.4 - - - +
997A CYS* 1.3 81.6 - - + +
999A ASP* 1.3 106.6 + - - +
1000A HIS 3.4 0.5 + - - -
1001A GLY* 3.8 4.5 + - - -
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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