Contacts of the strand formed by residues 98 - 111 (chain 2) in PDB entry 1ZBE
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 TYR 98 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532 THR* 5.3 1.9 + - - -
552 VAL* 5.8 0.7 - - + -
932 HIS* 6.0 0.4 - + - -
942 LEU* 3.0 33.3 + - + +
952 VAL* 3.8 13.5 - - - +
972 SER* 1.3 97.7 - - - +
992 ALA* 1.3 65.1 + - - +
1002 TYR* 3.3 5.9 + - - +
1012 MET* 4.7 3.8 - - + +
2102 VAL* 3.5 46.0 - - + -
2112 ALA* 3.8 10.8 - - - +
2122 GLY 3.3 5.6 - - - -
2132 GLU* 3.8 36.0 - - + +
2142 LEU* 3.5 9.3 - - - +
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Residues in contact with ALA 99 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982 TYR* 1.3 73.8 - - - +
1002 TYR* 1.3 89.4 + - + +
1692 ASP 4.0 3.8 - - - +
1702 GLN* 4.0 16.1 - - - +
2112 ALA 4.1 0.2 - - - +
2122 GLY 2.8 17.5 + - - +
2142 LEU* 3.7 7.4 - - + +
1273 PRO* 3.8 13.0 - - + -
1283 PRO 3.1 28.0 - - - +
1293 GLY* 5.4 1.1 - - - -
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Residues in contact with TYR 100 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482 THR* 6.1 0.2 - - + -
982 TYR* 3.3 0.9 - - - +
992 ALA* 1.3 96.6 - - + +
1012 MET* 1.3 65.7 + - - +
1682 TYR* 4.1 18.1 - - + -
1692 ASP 3.3 10.5 - - - +
1702 GLN* 3.5 33.9 + - + -
2102 VAL* 3.3 3.6 - - - +
2112 ALA* 2.8 41.3 + - + +
1273 PRO* 5.2 0.7 - - + -
1283 PRO* 3.2 28.3 - - + +
1633 VAL* 3.6 36.7 + - + -
1643 SER* 3.5 21.3 + - - -
1653 ALA* 3.5 25.5 + - + -
1813 VAL 4.6 2.1 + - - -
1823 GLN* 4.3 2.9 + - - -
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Residues in contact with MET 101 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912 PHE* 3.7 35.9 - - + -
942 LEU* 3.9 17.5 - - + -
952 VAL* 3.6 39.9 - - + -
982 TYR* 4.7 7.9 - - + +
1002 TYR* 1.3 80.1 - - - +
1022 ARG* 1.3 61.9 + - - +
1032 ASN* 4.6 1.6 - - - +
1682 TYR* 3.7 5.2 - - - -
1692 ASP* 2.8 36.8 + - - +
1712 TYR* 4.0 18.4 - - + +
2082 VAL* 4.2 14.6 - - + -
2092 HIS 3.2 7.6 - - - +
2102 VAL* 3.9 14.1 - - + -
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Residues in contact with ARG 102 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402 GLU* 3.3 23.6 + - - -
412 ASP* 3.1 43.4 + - - +
422 HIS 3.9 5.7 + - - -
432 VAL* 3.3 29.3 - - - +
1012 MET* 1.3 78.1 - - - +
1032 ASN* 1.3 65.4 + - - +
1622 TYR* 3.5 29.5 + - + +
1672 ARG* 3.0 36.5 + - - +
1682 TYR* 3.5 33.0 - - + -
1712 TYR* 3.8 7.9 - - - -
2072 TYR 3.4 1.4 + - - +
2082 VAL* 3.6 1.0 - - - +
2092 HIS* 3.0 36.8 + - + +
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Residues in contact with ASN 103 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402 GLU* 4.8 1.3 - - - -
912 PHE* 3.5 15.6 - - + -
1012 MET* 4.6 1.0 - - - +
1022 ARG* 1.3 79.2 + - - +
1042 GLY* 1.3 80.6 + - - +
1052 TRP* 3.7 21.7 + - - -
1622 TYR* 3.2 26.9 - - - +
1712 TYR* 2.8 36.1 + - - -
1772 TRP* 5.4 1.0 - - - -
2052 PRO* 3.6 12.7 - - - +
2062 THR 3.1 16.4 - - - +
2072 TYR* 3.7 4.7 - - - -
2082 VAL* 3.8 15.7 - - + -
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Residues in contact with GLY 104 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402 GLU* 3.9 6.3 + - - -
1032 ASN* 1.3 84.7 + - - +
1052 TRP* 1.3 63.1 + - - -
1602 VAL 3.5 10.5 - - - -
1612 PRO 4.1 1.1 - - - -
1622 TYR* 3.8 13.0 - - - -
2052 PRO* 3.4 1.2 - - - +
2062 THR* 2.8 42.6 + - - -
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Residues in contact with TRP 105 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622 PHE* 4.1 21.3 - + - -
832 LEU* 3.4 32.5 + - + +
842 PRO* 3.7 34.1 - - + -
912 PHE* 4.1 8.5 - + - -
1032 ASN* 3.7 19.5 + - - +
1042 GLY* 1.3 74.7 - - - -
1062 ASP* 1.3 60.1 + - - +
1072 VAL* 3.8 15.6 + - + +
1252 MET* 4.1 6.7 - - + -
1582 ILE 4.0 0.3 - - - +
1592 THR* 3.4 4.3 - - - +
1602 VAL* 2.9 45.0 + - + +
1712 TYR* 5.2 2.9 + - - -
1762 PRO* 5.6 2.6 - - + +
1772 TRP* 3.6 38.9 - + + +
2032 ILE* 3.7 16.8 - - + -
2042 ALA 3.6 2.9 - - - -
2052 PRO* 3.7 32.3 - - + -
2062 THR* 3.5 5.1 + - - -
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Residues in contact with ASP 106 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172 THR* 3.4 19.6 - - - +
192 ASN* 3.0 27.1 + - - +
612 PHE* 4.2 4.8 - - - -
1052 TRP* 1.3 73.4 - - - +
1072 VAL* 1.3 60.2 + - - +
1572 HIS* 2.7 29.3 + - - -
1582 ILE 3.9 0.9 - - - -
1592 THR* 2.7 21.4 + - + +
2022 ASN 4.1 1.2 - - - +
2032 ILE* 3.6 2.6 - - - -
2042 ALA* 2.8 36.0 + - + +
2062 THR* 4.0 13.9 - - + +
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Residues in contact with VAL 107 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832 LEU* 5.3 2.2 - - + -
1052 TRP* 4.1 11.2 - - + -
1062 ASP* 1.3 76.5 + - - +
1082 GLU* 1.3 65.2 + - - +
1092 VAL* 4.0 22.2 - - + -
1232 VAL* 5.6 0.9 - - + -
1252 MET* 3.8 32.5 - - + -
1572 HIS* 3.1 8.8 + - - -
1582 ILE* 2.8 52.2 + - + +
1602 VAL* 5.8 0.2 - - + -
1792 LEU* 4.3 19.3 - - + -
2022 ASN 4.0 2.0 - - - -
2032 ILE* 4.3 17.9 - - + +
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Residues in contact with GLU 108 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152 LEU* 5.9 0.7 - - - +
172 THR* 4.6 4.3 + - - -
242 SER* 2.7 34.5 + - - +
262 THR* 3.9 13.7 + - - -
612 PHE* 4.8 7.9 - - + -
1072 VAL* 1.3 78.3 - - - +
1092 VAL* 1.3 64.9 + - - +
1102 SER* 6.4 0.2 - - - -
1552 THR* 3.6 21.7 - - + +
1562 ALA 3.3 4.9 - - - +
1572 HIS* 4.2 21.6 - - + +
2002 TYR 4.3 0.2 - - - +
2012 ALA* 3.6 1.4 - - - -
2022 ASN* 2.8 58.5 + - + +
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Residues in contact with VAL 109 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662 LEU* 4.4 6.1 - - + -
1072 VAL* 4.0 8.9 - - + +
1082 GLU* 1.3 80.6 - - - +
1102 SER* 1.6 50.8 + - - +
1232 VAL* 4.4 13.9 - - + -
1482 ILE* 3.7 15.2 - - + +
1552 THR* 3.3 7.7 - - - -
1562 ALA* 2.7 49.1 + - + +
1792 LEU* 4.0 27.4 - - + -
1812 VAL* 4.6 8.1 - - + -
1992 VAL* 3.8 21.8 - - + -
2002 TYR 3.5 9.2 - - - +
2012 ALA* 4.3 6.7 - - + -
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Residues in contact with SER 110 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082 GLU* 6.4 0.2 - - - -
1092 VAL* 1.6 55.7 - - - +
1112 ALA* 1.3 65.0 - - - +
1122 VAL* 3.6 15.5 - - - +
1542 MET* 3.3 9.2 - - - -
1552 THR* 4.7 6.7 - - - +
1982 LYS 3.6 1.8 - - - +
1992 VAL* 3.2 8.6 - - - +
2002 TYR* 2.9 53.1 + - - +
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Residues in contact with ALA 111 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692 TRP* 4.6 4.2 - - + -
1102 SER* 1.3 80.8 - - - +
1122 VAL* 1.3 58.5 + - - +
1132 GLY 3.7 2.8 + - - -
1212 LEU* 4.1 12.3 - - + -
1482 ILE* 3.9 26.1 - - + +
1502 PRO* 5.6 4.0 - - - +
1532 ASN 4.9 0.3 - - - +
1542 MET* 2.9 23.2 + - - +
1972 ILE* 3.5 24.7 - - + +
1982 LYS 4.1 1.3 - - - -
1992 VAL* 4.0 14.1 - - + -
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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