Contacts of the helix formed by residues 987 - 1006 (chain A) in PDB entry 3H2U
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 ARG 987 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983A GLN* 3.5 23.8 + - - +
984A VAL* 3.1 48.8 + - - +
986A GLU* 1.3 77.8 - - - +
988A ILE* 1.3 65.3 + - - +
989A PRO* 3.3 3.4 - - - -
990A THR* 3.1 13.0 + - - -
991A ILE* 3.0 34.3 + - + +
1033A SER* 4.0 17.6 + - - +
1036A GLU* 4.4 9.3 + - - -
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Residues in contact with ILE 988 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A SER* 3.7 28.3 - - - +
961A VAL* 4.3 10.5 - - + -
962A THR* 3.3 21.5 - - - +
984A VAL 3.9 5.2 - - - +
985A CYS* 3.8 22.7 - - + +
987A ARG* 1.3 76.3 - - - +
989A PRO* 1.3 62.8 - - + +
991A ILE* 3.1 12.2 + - - +
992A SER* 2.9 29.0 + - - -
1030A LEU* 4.2 9.1 - - + +
1033A SER* 4.2 16.4 - - - +
1034A VAL* 4.3 15.5 - - + -
1037A THR* 3.4 25.1 - - - +
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Residues in contact with PRO 989 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A SER* 5.0 1.8 - - - +
959A ASP* 4.9 12.3 - - - +
962A THR* 4.1 20.4 - - + +
966A LYS* 5.7 3.1 - - - +
985A CYS 3.7 8.5 - - - +
986A GLU* 3.8 10.1 - - - +
987A ARG 3.3 4.7 - - - -
988A ILE* 1.3 95.4 - - + +
990A THR* 1.3 57.7 + - - +
992A SER* 3.4 8.7 + - - +
993A THR* 2.8 33.8 + - - -
1014C GLU* 6.0 2.7 - - - +
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Residues in contact with THR 990 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A GLU 4.5 8.1 + - - -
987A ARG* 3.1 12.3 + - - -
989A PRO* 1.3 77.4 - - - +
991A ILE* 1.3 68.6 - - + +
992A SER 3.1 0.3 + - - -
993A THR* 3.1 6.8 + - - -
994A GLN* 3.0 34.5 + - - +
1018C GLN* 3.5 34.0 + - - +
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Residues in contact with ILE 991 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987A ARG* 3.0 27.8 + - + +
988A ILE* 3.1 7.4 + - - +
990A THR* 1.3 78.2 - - + +
992A SER* 1.3 57.6 + - - +
994A GLN* 3.5 3.0 + - - -
995A LEU* 3.0 10.9 + - - +
1026A ASN* 2.8 64.3 + - - +
1029A ASN* 4.0 19.3 - - + +
1030A LEU* 3.7 18.6 - - + +
1033A SER* 3.4 31.2 - - - +
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Residues in contact with SER 992 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955A ALA* 4.3 18.0 - - - +
958A SER* 2.7 32.6 + - - -
959A ASP* 5.7 1.6 - - - -
988A ILE 2.9 12.4 + - - -
989A PRO* 3.4 12.1 - - - -
990A THR 3.1 0.2 - - - -
991A ILE* 1.3 75.2 - - - +
993A THR* 1.3 65.9 + - - +
995A LEU* 3.0 18.6 + - - +
996A LYS* 3.0 18.9 + - - +
1030A LEU* 4.0 10.2 - - - +
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Residues in contact with THR 993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A PRO 2.8 21.3 + - - -
990A THR* 3.7 6.4 - - - -
992A SER* 1.3 75.3 - - - +
994A GLN* 1.3 63.4 + - - +
996A LYS* 3.0 27.4 + - - +
997A ILE* 3.1 14.2 + - + +
1014C GLU* 3.6 17.5 + - + +
1015C GLU* 3.5 41.3 - - + +
1018C GLN* 3.6 23.4 + - + -
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Residues in contact with GLN 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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990A THR* 3.0 25.8 + - - +
991A ILE* 5.1 1.3 - - - -
993A THR* 1.3 75.4 - - - +
995A LEU* 1.3 53.0 + - - +
997A ILE* 3.3 9.5 + - - +
998A LEU* 2.7 44.0 + - + +
1026A ASN* 3.4 24.2 + - - +
1018C GLN* 2.6 33.3 + - + -
1022C MET* 3.6 28.8 - - - +
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Residues in contact with LEU 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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930A MET* 4.6 2.5 - - + -
933A MET* 4.3 11.4 - - + -
951A ALA* 4.5 7.0 - - + +
954A ILE* 3.8 30.5 - - + -
955A ALA 5.1 0.4 - - - +
991A ILE 3.0 9.4 + - - +
992A SER* 3.0 16.2 + - - +
994A GLN* 1.3 72.5 - - - +
996A LYS* 1.3 55.8 + - - +
998A LEU* 4.6 2.0 - - - -
999A SER* 2.6 43.8 + - - +
1023A LEU* 3.5 27.4 - - + -
1026A ASN* 3.4 19.7 + - - +
1027A ALA* 4.4 16.2 - - - +
1030A LEU* 3.7 26.9 - - + -
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Residues in contact with LYS 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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951A ALA* 4.0 20.0 - - + +
952A LYS* 4.2 20.4 - - + -
955A ALA* 3.7 29.2 - - + -
992A SER* 3.0 10.5 + - - +
993A THR* 3.0 25.1 + - - +
995A LEU* 1.3 76.7 - - - +
997A ILE* 1.3 64.5 + - - +
999A SER* 3.5 1.2 - - - -
1000A THR* 2.9 31.6 + - - +
1012C SER* 4.3 3.6 + - - -
1014C GLU* 5.6 5.7 + - - -
1015C GLU* 2.8 46.7 + - - +
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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 THR* 3.1 30.5 + - + +
994A GLN 3.5 5.2 - - - +
996A LYS* 1.3 76.1 - - - +
998A LEU* 1.3 65.2 + - + +
1000A THR* 3.5 6.3 + - - -
1001A VAL* 3.0 26.7 + - - +
998C LEU* 5.4 1.6 - - + -
1001C VAL* 3.9 27.9 - - + +
1005C MET* 4.0 20.0 - - + -
1015C GLU* 3.3 30.5 + - + +
1018C GLN* 3.9 1.6 - - + -
1019C ALA* 3.7 4.9 - - + +
1022C MET* 3.0 40.2 - - + -
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Residues in contact with LEU 998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A GLN* 2.7 29.8 + - + +
995A LEU 4.0 0.2 - - - +
997A ILE* 1.3 78.7 - - + +
999A SER* 1.3 66.2 + - - +
1001A VAL* 3.1 9.5 + - + +
1002A LYS* 2.9 23.6 + - - +
1019A ALA* 5.3 2.5 - - - +
1022A MET* 3.9 42.0 - - + +
1023A LEU* 4.0 21.4 - - + +
1026A ASN* 3.8 34.3 - - + +
997C ILE* 5.4 3.8 - - + -
998C LEU* 4.7 13.5 - - + -
1022C MET* 5.0 5.6 - - - -
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Residues in contact with SER 999 (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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933A MET* 3.3 13.5 - - - +
947A LEU* 3.6 20.8 - - - +
948A ILE* 4.8 1.8 - - - -
951A ALA* 2.9 29.2 - - - +
995A LEU 2.6 29.2 + - - -
996A LYS 3.5 1.6 - - - -
998A LEU* 1.3 71.6 - - - +
1000A THR* 1.3 53.5 + - - +
1002A LYS 3.3 0.9 + - - -
1003A ALA* 2.6 38.0 + - - +
1023A LEU* 3.9 16.9 - - - +
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Residues in contact with THR1000 (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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948A ILE* 3.9 27.8 - - + +
996A LYS* 2.9 19.8 + - - +
997A ILE* 3.5 6.3 - - - -
999A SER* 1.3 74.5 - - - +
1001A VAL* 1.3 64.6 + - - +
1003A ALA* 3.5 6.6 - - - +
1004A THR* 2.7 42.4 + - + +
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Residues in contact with VAL1001 (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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997A ILE* 3.0 14.7 + - + +
998A LEU* 3.1 13.7 + - + +
1000A THR* 1.3 74.1 - - + +
1002A LYS* 1.3 66.1 + - - +
1004A THR* 2.8 28.3 + - - -
1005A MET* 3.1 20.5 + - + +
1019A ALA* 3.8 25.4 - - + -
1022A MET* 5.7 0.2 - - + -
997C ILE* 4.0 22.0 - - + +
1001C VAL* 3.0 37.5 - - + -
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Residues in contact with LYS1002 (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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937A VAL* 3.8 33.3 + - + -
947A LEU* 4.1 4.7 - - + -
998A LEU 2.9 15.6 + - - +
999A SER 3.7 3.6 - - - +
1001A VAL* 1.3 77.7 - - - +
1003A ALA* 1.3 62.6 + - - +
1005A MET* 3.1 14.3 + - + +
1006A LEU* 3.0 50.5 + - + +
1016A SER* 4.0 15.0 + - - +
1019A ALA* 4.4 10.8 - - + -
1020A THR* 2.5 38.9 + - - +
1023A LEU* 3.8 13.0 - - + -
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Residues in contact with ALA1003 (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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944A LYS* 3.5 27.3 - - - +
947A LEU* 3.8 12.5 - - + +
948A ILE* 3.4 36.6 - - + -
999A SER 2.6 21.2 + - - +
1000A THR 3.5 2.5 - - - +
1002A LYS* 1.3 72.5 - - - +
1004A THR* 1.3 61.4 + - - +
1006A LEU* 3.4 23.5 + - - +
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Residues in contact with THR1004 (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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944A LYS* 3.8 24.0 + - - +
948A ILE* 5.6 0.4 - - + -
1000A THR* 2.7 34.3 - - + +
1001A VAL* 2.8 17.8 + - - +
1003A ALA* 1.3 76.3 - - + +
1005A MET* 1.3 67.4 + - - +
1006A LEU 4.2 1.4 - - - +
1008A ARG* 3.3 24.6 + - - +
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Residues in contact with MET1005 (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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1001A VAL* 3.1 29.3 + - + +
1002A LYS* 3.1 11.2 + - + +
1004A THR* 1.3 83.6 - - - +
1006A LEU* 1.3 66.9 + - - +
1007A GLY 3.0 3.3 + - - -
1008A ARG* 3.3 24.1 + - - +
1011A ILE* 3.8 35.3 - - + +
1015A GLU* 4.1 15.3 - - - +
1016A SER* 3.6 31.9 - - - -
1019A ALA* 3.7 13.2 - - - -
997C ILE* 4.3 12.6 - - + -
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Residues in contact with LEU1006 (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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936A LEU 3.7 12.8 - - - +
937A VAL 4.1 2.2 - - - +
939A GLY* 3.6 24.0 - - - +
940A GLY 5.6 0.4 - - - +
943A THR* 3.1 41.1 - - - +
944A LYS* 4.2 7.4 - - + +
947A LEU* 4.1 16.6 - - + -
1002A LYS* 3.0 42.5 + - + +
1003A ALA* 3.5 13.8 - - - +
1004A THR 3.4 1.6 - - - +
1005A MET* 1.3 74.1 - - - +
1007A GLY* 1.3 57.3 + - - +
1008A ARG* 3.5 8.0 + - - +
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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