Contacts of the strand formed by residues 1025 - 1035 (chain A) in PDB entry 2ZM3
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 GLU1025 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020A GLY* 4.3 9.5 + - - -
1022A VAL* 3.3 34.0 + - + +
1023A LYS 3.1 6.6 - - - +
1024A ASP* 1.3 80.0 - - - +
1026A PRO* 1.3 71.0 - - + +
1027A GLU* 3.5 14.8 + - - +
1028A THR* 3.3 27.6 + - - +
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Residues in contact with PRO1026 (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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1019A LYS* 3.4 7.8 - - - +
1020A GLY* 3.0 23.4 + - - -
1024A ASP 3.6 8.1 - - - +
1025A GLU* 1.3 86.7 - - + +
1027A GLU* 1.3 67.8 + - + +
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Residues in contact with GLU1027 (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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1017A VAL* 4.0 19.5 - - + +
1018A ALA 3.3 5.6 - - - -
1019A LYS* 3.5 38.5 + - + +
1025A GLU* 3.8 15.4 - - - +
1026A PRO* 1.3 89.7 - - + +
1028A THR* 1.3 67.6 + - - +
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Residues in contact with THR1028 (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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1017A VAL* 3.4 4.4 - - - -
1018A ALA 2.8 34.9 + - - -
1021A VAL* 4.2 4.2 + - - +
1022A VAL* 3.2 34.5 + - + +
1025A GLU* 3.3 21.7 + - - +
1027A GLU* 1.3 79.2 + - - +
1029A ARG* 1.3 77.0 + - - +
1030A VAL* 3.5 10.3 - - + +
1066A LEU* 5.0 2.9 - - + -
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Residues in contact with ARG1029 (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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1003A ARG* 5.1 3.2 - - - +
1015A GLU* 2.8 33.1 + - - +
1016A GLY 3.4 8.1 - - - +
1017A VAL* 4.5 10.8 - - + +
1028A THR* 1.3 83.4 - - - +
1030A VAL* 1.3 63.5 + - - +
1066A LEU* 5.3 0.2 - - - +
1080A GLU* 5.3 0.3 - - - -
1081A LEU* 3.5 35.2 + - + +
1083A THR* 3.8 22.0 - - - +
1145A GLU* 4.8 6.1 + - - +
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Residues in contact with VAL1030 (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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1015A GLU* 3.5 9.0 - - - +
1016A GLY 2.8 44.3 + - - +
1017A VAL 4.2 2.2 - - - +
1018A ALA* 3.9 15.9 - - + +
1028A THR* 3.5 13.2 - - - +
1029A ARG* 1.3 81.5 - - - +
1031A ALA* 1.3 58.5 + - - +
1032A ILE* 3.6 28.0 - - + -
1066A LEU* 3.8 17.3 - - + -
1078A ILE* 3.6 22.0 - - + -
1079A MET 3.3 9.0 - - - +
1081A LEU* 3.7 9.9 - - - +
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Residues in contact with ALA1031 (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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1A 575 3.4 48.2 - - + +
1005A LEU* 4.2 5.6 - - + -
1013A VAL* 4.3 4.3 - - + -
1014A TYR 3.3 8.1 - - - +
1030A VAL* 1.3 74.1 - - - +
1032A ILE* 1.3 62.2 - - - +
1033A LYS 4.1 0.2 - - - -
1077A VAL 3.7 1.0 - - - +
1078A ILE* 3.6 2.4 - - - -
1079A MET* 2.7 40.0 + - + +
1080A GLU 3.9 4.3 - - - +
1081A LEU* 4.0 1.4 - - + +
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Residues in contact with ILE1032 (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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999A ILE* 3.5 28.3 - - + -
1001A MET* 4.0 23.8 - - + -
1012A MET 3.9 1.2 - - - +
1013A VAL* 3.3 4.8 - - - -
1014A TYR* 2.7 49.6 + - + +
1015A GLU 4.4 0.2 - - - -
1016A GLY* 4.3 10.5 - - - +
1030A VAL* 3.6 26.2 - - + -
1031A ALA* 1.3 74.3 - - - +
1033A LYS* 1.3 64.5 + - - +
1034A THR* 4.3 1.8 - - + -
1076A LEU* 3.8 35.0 - - + -
1077A VAL 3.8 2.0 - - - +
1078A ILE* 4.1 13.2 - - + -
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Residues in contact with LYS1033 (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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1A 575 4.1 25.6 - - + -
1008A GLY* 6.0 2.0 - - - -
1010A PHE* 6.5 1.1 - - + -
1012A MET 4.2 3.6 - - - -
1013A VAL* 4.2 19.5 - - + +
1031A ALA 5.3 0.4 - - - -
1032A ILE* 1.3 76.2 - - - +
1034A THR* 1.3 62.2 + - - +
1047A PHE* 3.9 22.2 - - + -
1050A GLU* 4.9 11.9 + - - +
1054A MET* 4.5 14.6 - - - +
1075A THR 3.6 0.2 - - - +
1076A LEU* 3.3 8.3 - - - +
1077A VAL* 3.0 46.3 + - - +
1079A MET* 3.7 35.0 - - + +
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Residues in contact with THR1034 (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 MET* 4.5 4.5 - - - -
1010A PHE 3.9 0.5 - - - +
1011A GLY* 3.7 19.8 + - - -
1012A MET* 3.1 23.9 + - - +
1014A TYR* 3.7 31.9 + - + -
1032A ILE* 4.3 3.1 - - + -
1033A LYS* 1.3 77.1 - - - +
1035A VAL* 1.3 69.3 + - - +
1036A ASN* 4.7 8.2 + - - -
1047A PHE* 4.5 3.6 - - - -
1074A PRO* 4.5 13.2 - - + -
1075A THR 3.4 4.9 - - - -
1076A LEU* 3.5 24.9 - - + -
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Residues in contact with VAL1035 (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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1010A PHE* 3.7 20.2 - - + +
1011A GLY* 5.6 0.2 - - - -
1034A THR* 1.3 78.7 - - - +
1036A ASN* 1.3 58.9 + - - +
1039A ALA* 3.7 16.8 - - + -
1043A GLU* 5.2 1.6 - - + +
1044A ARG* 3.0 53.3 + - + +
1047A PHE* 3.3 45.1 - - + -
1073A GLN* 3.2 0.5 - - - +
1074A PRO* 3.3 2.9 - - - +
1075A THR* 3.1 27.1 + - - +
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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