Contacts of the strand formed by residues 999 - 1007 (chain D) 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 ILE 999 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994D VAL* 3.9 13.9 - - + -
995D ALA 3.9 12.1 - - - +
996D ARG* 3.0 19.6 + - - +
997D GLU 3.1 3.4 - - - +
998D LYS* 1.3 82.2 - - - +
1000D THR* 1.3 72.0 + - - +
1001D MET* 4.3 6.4 - - + +
1017D VAL 3.7 1.3 - - - +
1018D ALA* 3.5 28.3 - - + -
1032D ILE* 3.6 26.2 - - + -
1069D VAL* 3.9 18.2 - - + -
1076D LEU* 4.1 15.7 - - + -
1078D ILE* 3.9 17.7 - - + -
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Residues in contact with THR1000 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105A ALA* 3.6 27.4 - - + -
997D GLU 5.1 2.9 + - - -
998D LYS 5.1 1.2 + - - -
999D ILE* 1.3 77.9 + - - +
1001D MET* 1.3 68.0 + - - +
1002D SER* 6.0 1.1 - - - -
1016D GLY* 3.1 5.5 - - - -
1017D VAL* 2.9 46.8 + - + +
1019D LYS* 5.8 4.5 + - - -
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Residues in contact with MET1001 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096A PRO* 5.9 3.8 - - + -
1105A ALA* 3.5 24.9 - - - +
1106A PRO* 3.6 24.0 + - + +
999D ILE* 4.6 10.8 - - + -
1000D THR* 1.3 79.4 - - - +
1002D SER* 1.3 61.3 + - - +
1014D TYR* 3.6 47.1 - - + -
1015D GLU 3.8 6.3 - - - +
1016D GLY* 4.3 0.2 - - - -
1032D ILE* 4.0 27.8 - - + -
1034D THR* 4.5 7.0 - - + -
1074D PRO* 6.3 2.7 - - + -
1076D LEU* 4.7 7.4 - - + -
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Residues in contact with SER1002 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094A LEU 5.7 0.2 - - - +
1096A PRO* 3.8 20.2 - - - +
1104A LEU 5.5 5.5 - - - +
1106A PRO* 5.9 1.1 - - - +
1000D THR* 5.3 1.6 - - - -
1001D MET* 1.3 77.1 - - - +
1003D ARG* 1.3 73.1 + - - +
1014D TYR* 5.1 0.4 - - - +
1015D GLU* 2.9 26.4 + - - +
1016D GLY* 4.7 3.8 - - - -
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Residues in contact with ARG1003 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096A PRO* 4.1 10.3 - - - +
1D 575 3.8 35.8 + - - -
1002D SER* 1.3 88.6 + - - +
1004D GLU* 1.3 68.2 + - - +
1005D LEU* 3.7 8.5 - - - +
1014D TYR* 3.1 12.6 - - - +
1015D GLU* 2.8 60.2 + - + +
1029D ARG* 5.6 2.6 - - - +
1083D THR* 5.0 2.6 + - - +
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Residues in contact with GLU1004 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096A PRO* 3.9 13.4 + - + +
1097A GLU* 3.5 33.8 - - - +
1003D ARG* 1.3 86.1 + - - +
1005D LEU* 1.3 62.0 + - - +
1006D GLY* 4.6 1.1 - - - +
1012D MET* 4.0 30.7 - - + +
1013D VAL 3.6 5.2 - - - -
1014D TYR* 3.6 23.6 + - + -
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Residues in contact with LEU1005 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D 575 3.5 69.2 - - + +
1003D ARG* 3.7 26.0 - - - +
1004D GLU* 1.3 73.8 - - - +
1006D GLY* 1.3 59.4 + - - +
1013D VAL* 2.7 18.2 + - + +
1014D TYR 3.6 6.7 - - - +
1015D GLU* 3.4 40.4 - - + +
1031D ALA* 4.1 7.4 - - + -
1081D LEU* 3.8 19.5 - - + -
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Residues in contact with GLY1006 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D 575 4.4 5.4 - - - -
1004D GLU* 3.6 2.0 - - - +
1005D LEU* 1.3 81.6 - - - +
1007D GLN* 1.3 64.8 + - - -
1012D MET* 3.6 10.6 - - - -
1013D VAL* 2.8 30.0 + - - +
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Residues in contact with GLN1007 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D 575 3.3 12.0 - - - +
1006D GLY* 1.3 71.2 - - - -
1008D GLY* 1.3 70.9 + - - +
1011D GLY* 3.3 32.6 + - - +
1012D MET* 3.2 28.0 + - + +
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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