Contacts of the helix formed by residues 1038 - 1051 (chain A) in PDB entry 4Z4Q
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 LYS1038 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028A ARG 3.5 18.4 - - - +
1029A ALA* 3.5 20.3 + - - +
1030A LEU 4.3 4.7 - - - +
1031A PRO* 4.4 9.9 - - + -
1037A LEU* 1.3 75.8 - - - +
1039A PRO* 1.3 78.4 - - + +
1040A VAL* 3.3 10.3 - - + +
1041A GLN* 2.7 43.0 + - + +
1042A ARG* 3.0 11.2 + - - -
1167A SER* 3.9 15.0 - - - +
1168A THR 2.7 31.9 + - - -
1169A GLY 3.6 3.4 - - - +
1170A ILE 5.6 0.2 - - - +
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Residues in contact with PRO1039 (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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1026A GLN 4.4 4.3 - - - +
1027A ASP* 3.7 39.0 - - + +
1028A ARG* 3.8 15.5 - - - +
1030A LEU 4.5 5.6 - - - +
1037A LEU 4.7 0.4 - - - +
1038A LYS* 1.3 88.1 - - + -
1040A VAL* 1.3 64.0 + - - +
1042A ARG* 3.2 21.7 + - - +
1043A ARG* 2.8 50.4 + - - +
1074A HIS* 5.2 2.0 - - + -
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Residues in contact with VAL1040 (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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1028A ARG 5.7 1.8 - - - +
1038A LYS* 4.6 11.2 - - + +
1039A PRO* 1.3 80.0 - - - +
1041A GLN* 1.3 74.0 + - + +
1043A ARG* 3.4 2.5 + - - +
1044A ILE* 2.8 44.0 + - + +
1069A ILE* 5.9 0.4 - - + -
1074A HIS* 3.7 40.7 - - + +
1080A SER* 4.8 2.7 - - - +
1081A ILE* 4.3 12.1 - - + +
1084A ALA* 4.1 16.4 - - + -
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Residues in contact with GLN1041 (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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1036A GLY 4.2 2.6 - - - +
1037A LEU* 3.6 21.8 - - + +
1038A LYS* 2.7 54.0 + - - +
1040A VAL* 1.3 85.3 - - + +
1042A ARG* 1.3 65.2 + - - +
1044A ILE* 3.1 4.9 + - - +
1045A LEU* 2.9 27.2 + - - +
1084A ALA* 5.1 3.9 + - + +
1087A ARG* 5.3 8.9 - - - +
1088A MET* 3.9 37.0 - - + +
1094A ASN* 6.0 1.8 - - - +
1167A SER* 5.5 0.9 + - - -
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Residues in contact with ARG1042 (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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1032A ASP* 3.7 13.7 - - - +
1035A ASP* 3.1 27.7 + - - -
1037A LEU* 3.4 37.1 + - + +
1038A LYS 3.0 7.5 + - - +
1039A PRO* 3.6 25.7 - - - +
1041A GLN* 1.3 75.7 - - - +
1043A ARG* 1.3 58.4 + - + +
1045A LEU* 3.3 1.6 + - - +
1046A TYR* 2.8 28.1 + - + +
1152A PRO* 3.5 26.5 + - + +
1153A THR* 3.6 15.8 + - - +
1154A VAL* 3.4 15.8 - - - +
1155A LEU* 3.5 27.1 - - + -
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Residues in contact with ARG1043 (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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1023A TYR* 5.2 5.1 + - - -
1027A ASP* 5.9 2.2 + - - +
1039A PRO* 2.8 36.0 + - - +
1040A VAL* 3.8 3.6 - - - +
1042A ARG* 1.3 72.2 - - + +
1044A ILE* 1.3 66.8 + - - +
1046A TYR* 4.6 4.9 - - + -
1047A SER* 3.0 29.0 + - - -
1069A ILE* 4.5 11.0 - - + -
1073A PHE* 3.6 33.7 + - + -
1074A HIS* 2.8 50.7 + - + +
1075A PRO* 4.1 7.1 - - - +
1076A HIS* 5.1 1.0 - - - -
1151A GLU* 2.8 40.9 + - + +
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Residues in contact with ILE1044 (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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1040A VAL* 2.8 26.0 + - + +
1041A GLN 3.1 6.5 + - - +
1043A ARG* 1.3 72.7 - - - +
1045A LEU* 1.3 62.0 + - + +
1047A SER* 4.2 0.2 - - - -
1048A MET* 3.2 50.7 + - - +
1069A ILE* 3.8 24.9 - - + +
1081A ILE* 3.6 17.5 - - + +
1084A ALA* 3.6 10.1 - - + -
1085A MET* 3.6 28.9 - - + +
1088A MET* 3.1 37.0 - - + -
1099A VAL* 4.8 4.3 - - + -
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Residues in contact with LEU1045 (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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1037A LEU* 4.0 16.2 - - + -
1041A GLN 2.9 16.9 + - - +
1042A ARG 4.0 2.2 - - - +
1044A ILE* 1.3 73.7 - - + +
1046A TYR* 1.3 62.3 + - - +
1048A MET 3.4 0.5 + - - -
1049A ASN* 2.8 33.8 + - - +
1088A MET* 4.6 6.5 - - - -
1098A LEU* 4.2 28.3 - - + +
1099A VAL* 4.5 7.6 - - + -
1123A LEU* 3.4 30.3 - - + +
1127A ALA* 4.4 8.7 - - + +
1130A LEU* 3.7 32.1 - - + -
1131A LEU* 4.5 7.4 - - + -
1155A LEU* 4.1 12.3 - - + -
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Residues in contact with TYR1046 (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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1042A ARG 2.8 21.8 + - - +
1043A ARG* 4.2 4.5 - - + +
1045A LEU* 1.3 73.4 - - - +
1047A SER* 1.3 57.8 + - - +
1049A ASN* 3.3 4.3 + - - +
1050A LYS* 2.9 50.3 + - + +
1073A PHE* 3.8 35.7 - + - -
1131A LEU* 4.3 10.2 - - + +
1134A ILE* 3.9 27.8 - - + -
1141A PHE* 3.8 17.2 - + - -
1149A GLU* 5.3 0.9 + - - +
1150A LYS 4.0 7.4 + - - -
1151A GLU* 4.8 0.4 - - + -
1152A PRO* 3.5 41.3 - - + -
1155A LEU* 4.7 2.9 - - + +
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Residues in contact with SER1047 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043A ARG 3.0 18.4 + - - -
1046A TYR* 1.3 76.7 - - - +
1048A MET* 1.3 66.9 + - - +
1050A LYS* 3.2 4.6 + - - +
1051A ASP* 3.1 38.0 + - - +
1065A SER 4.5 0.7 + - - -
1068A ASN* 4.1 5.4 - - - +
1069A ILE* 3.6 30.8 + - - +
1072A ASN* 5.2 0.5 + - - -
1073A PHE* 3.8 27.4 - - - -
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Residues in contact with MET1048 (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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1044A ILE* 3.2 37.4 + - + +
1047A SER* 1.3 77.8 - - - +
1049A ASN* 1.3 61.6 + - - +
1051A ASP* 3.2 8.3 + - - -
1053A ASN* 3.1 55.9 + - + +
1065A SER* 4.4 17.3 - - - +
1069A ILE* 5.0 3.8 - - + -
1085A MET* 4.4 15.0 - - - +
1099A VAL* 4.7 4.9 - - + -
1121A ALA* 4.3 8.1 - - + -
1122A ARG* 3.6 34.1 - - - +
1123A LEU* 3.7 20.9 - - + +
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Residues in contact with ASN1049 (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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1045A LEU 2.8 19.1 + - - +
1046A TYR* 3.7 6.8 - - + +
1048A MET* 1.3 79.5 - - - +
1050A LYS* 1.3 63.9 + - - +
1052A SER* 3.0 15.4 + - - -
1054A THR* 4.0 19.6 - - - +
1123A LEU* 3.8 6.1 - - + +
1128A GLY* 5.6 3.8 - - - -
1131A LEU* 3.3 39.9 - - + +
1134A ILE* 4.3 14.0 - - - +
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Residues in contact with LYS1050 (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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1046A TYR* 2.9 45.0 + - + +
1047A SER* 3.6 6.7 - - - +
1049A ASN* 1.3 78.8 - - - +
1051A ASP* 1.3 66.6 + - - +
1052A SER* 3.3 6.3 + - - -
1072A ASN* 5.9 1.6 - - - +
1073A PHE* 4.6 4.5 - - + -
1149A GLU* 3.4 25.6 - - - +
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Residues in contact with ASP1051 (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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1047A SER* 3.1 26.4 + - - +
1048A MET* 3.7 7.7 - - - +
1049A ASN 3.0 1.4 - - - -
1050A LYS* 1.3 91.2 - - - +
1052A SER* 1.3 56.1 + - - +
1053A ASN* 3.1 3.3 + - + -
1060A ARG* 2.7 43.3 + - - +
1065A SER* 5.7 1.4 - - - -
1068A ASN* 3.2 29.4 + - - +
1072A ASN* 5.8 2.1 + - - -
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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
------------------------------------------------------------
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