Contacts of the strand formed by residues 992 - 998 (chain E) in PDB entry 3T06
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 LEU 992 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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956E PHE* 3.6 24.5 - - + -
959E LEU* 4.7 9.9 - - + -
964E ARG* 3.3 43.5 - - - +
987E LEU 3.8 0.7 - - - +
988E LEU* 3.5 4.2 - - - +
989E LEU* 3.0 42.7 + - + +
990E GLU 3.8 0.2 - - - -
991E ASP* 1.3 92.4 + - - +
993E LEU* 1.3 60.6 + - - +
994E VAL* 3.9 7.0 - - + -
1025E VAL* 3.5 25.6 - - + -
1026E LEU 3.4 8.7 - - - +
1027E LYS* 4.3 9.9 - - + -
1028E LEU* 3.8 5.8 - - - +
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Residues in contact with LEU 993 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986E VAL* 3.8 19.3 - - + -
987E LEU 3.6 13.0 - - - +
988E LEU* 4.1 19.3 - - + -
992E LEU* 1.3 72.9 - - - +
994E VAL* 1.3 60.4 + - - +
995E LEU* 4.5 14.4 - - + -
1025E VAL* 3.6 2.6 - - - -
1026E LEU* 3.0 57.9 + - + +
1028E LEU* 3.9 14.9 - - + +
1045E ILE* 3.9 30.1 - - + -
1057E TYR* 6.4 0.2 - - + -
1059E LEU* 5.1 4.3 - - + -
1070E TRP* 4.5 1.6 - - + -
1074E LEU* 4.4 11.7 - - + -
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Residues in contact with VAL 994 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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959E LEU* 4.7 9.4 - - + -
961E LEU* 5.1 3.8 - - + -
985E HIS 4.0 0.3 - - - +
986E VAL* 3.1 8.3 - - - +
987E LEU* 2.9 45.5 + - + +
989E LEU* 3.5 30.7 - - + -
992E LEU* 4.2 8.7 - - + -
993E LEU* 1.3 75.5 - - - +
995E LEU* 1.3 65.2 + - - +
996E LEU* 3.7 30.1 + - + -
1005E LEU* 3.9 17.9 - - + -
1024E PRO 4.0 1.8 - - - -
1025E VAL* 4.2 13.2 - - + +
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Residues in contact with LEU 995 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974E TRP* 3.9 23.8 - - + -
984E LEU* 3.8 25.6 - - + +
985E HIS 4.5 0.7 - - - -
986E VAL* 3.6 31.4 - - + -
993E LEU* 4.5 14.1 - - + -
994E VAL* 1.3 74.7 - - - +
996E LEU* 1.3 63.9 + - - +
997E GLN 4.1 0.5 + - - -
1004E LEU 4.2 0.3 - - - +
1005E LEU* 3.9 18.9 - - - +
1006E LYS 5.0 0.2 + - - -
1008E HIS* 5.5 4.3 + - - +
1024E PRO* 3.0 28.6 + - + +
1026E LEU* 4.3 10.3 - - + -
1057E TYR* 4.0 22.4 - - + -
1059E LEU* 4.8 8.7 - - + -
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Residues in contact with LEU 996 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936E TYR* 5.6 1.1 - - + -
940E LEU* 4.1 17.0 - - + -
961E LEU* 5.3 6.1 - - + -
984E LEU* 3.3 7.7 - - - +
985E HIS* 2.6 53.9 + - + +
987E LEU* 4.1 31.9 - - + -
994E VAL* 3.7 23.1 - - + +
995E LEU* 1.3 72.2 - - - +
997E GLN* 1.3 60.0 + - - +
1003E LEU* 4.2 34.3 - - + -
1004E LEU 4.0 2.0 - - - -
1005E LEU* 3.8 27.1 - - + +
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Residues in contact with GLN 997 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982E LEU* 3.8 25.4 - - - +
983E ASP 4.4 15.2 + - - +
984E LEU* 4.5 5.1 - - + +
995E LEU 4.1 0.2 + - - -
996E LEU* 1.3 73.6 - - - +
998E LYS* 1.3 74.5 + - - +
999E GLN* 3.4 5.5 + - - +
1003E LEU* 3.6 6.4 - - - -
1004E LEU* 3.3 49.0 + - + +
1006E LYS* 4.6 8.3 - - - +
1008E HIS* 3.1 34.0 - - + +
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Residues in contact with LYS 998 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971E PRO* 4.8 14.1 - - + +
983E ASP* 3.8 22.8 - - + +
984E LEU 4.3 12.6 - - - +
985E HIS* 3.8 33.5 + - + +
996E LEU 3.9 0.6 + - - -
997E GLN* 1.3 80.0 - - - +
999E GLN* 1.3 65.3 + - - +
1002E LYS 4.1 3.4 - - - -
1003E LEU* 4.7 10.5 - - + -
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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