Contacts of the strand formed by residues 97 - 104 (chain 1) in PDB entry 3TDD
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 ASN 97 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451 ILE* 3.7 21.6 - - + +
461 SER 3.1 20.7 + - - +
471 GLY* 3.7 1.3 - - - -
481 ASP 2.9 28.1 + - - +
511 ASP* 3.3 20.1 - - - +
521 MET* 4.0 1.6 - - - +
551 ILE* 3.5 15.0 - - - +
871 MET* 3.9 4.4 - - + +
951 LEU* 2.7 17.1 + - - +
961 TRP* 1.3 78.5 + - - +
981 ALA* 1.3 60.2 + - - +
991 ILE* 4.2 10.8 - - + -
1141 ASN* 3.2 4.2 - - - +
1151 LEU* 2.8 31.4 + - - +
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Residues in contact with ALA 98 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441 GLY 4.0 0.7 - - - +
451 ILE* 3.7 0.7 - - - -
461 SER* 2.9 46.8 + - - +
971 ASN* 1.3 73.6 - - - +
991 ILE* 1.3 61.8 + - - +
1121 TYR* 4.1 13.7 - - + +
1131 VAL 3.8 4.0 - - - -
1141 ASN* 4.1 4.3 - - + -
1271 THR* 3.6 24.7 - - + +
1281 GLY 5.4 1.1 - - - +
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Residues in contact with ILE 99 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431 VAL* 3.4 29.6 - - + -
441 GLY 3.4 4.0 - - - +
451 ILE* 4.1 10.5 - - + -
551 ILE* 3.8 27.8 - - + -
831 LEU* 4.3 20.4 - - + -
871 MET* 4.1 21.1 - - + -
971 ASN* 4.2 9.0 - - + -
981 ALA* 1.3 81.0 - - - +
1001 ILE* 1.3 71.7 + - - +
1011 VAL* 4.3 2.5 - - + -
1111 ARG 4.0 0.2 - - - +
1121 TYR* 3.2 6.8 - - - -
1131 VAL* 2.7 54.7 + - + +
1271 THR* 4.6 0.4 - - - +
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Residues in contact with ILE 100 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31 VAL* 3.5 24.0 - - + +
51 SER* 3.5 17.9 - - - +
141 ILE* 3.9 16.5 - - + +
431 VAL* 3.6 1.4 - - - -
441 GLY 2.8 36.3 + - - +
991 ILE* 1.3 80.3 - - - +
1011 VAL* 1.3 65.4 + - - +
1021 ALA 3.8 0.7 + - - -
1101 LEU* 4.0 15.3 - - + -
1111 ARG 3.4 7.9 - - - +
1121 TYR* 4.1 11.0 - - + -
1251 LEU* 3.3 38.1 - - + +
1261 ALA* 3.9 3.4 - - - +
1271 THR* 3.9 15.7 - - + -
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Residues in contact with VAL 101 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411 THR* 3.8 25.1 - - + -
421 VAL 3.9 2.5 - - - -
431 VAL* 4.1 15.9 - - + -
761 PRO* 4.0 12.1 - - + +
791 ILE* 4.9 0.7 - - + -
801 PHE* 3.7 37.5 - - + +
831 LEU* 4.3 13.2 - - + -
991 ILE* 4.3 6.3 - - + -
1001 ILE* 1.3 75.9 - - - +
1021 ALA* 1.3 60.5 + - - +
1091 PHE* 3.5 19.4 - - + -
1101 LEU* 3.4 7.3 - - - +
1111 ARG 2.9 28.9 + - - -
1131 VAL* 5.7 0.4 - - + -
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Residues in contact with ALA 102 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121 VAL* 3.7 15.0 - - + -
141 ILE* 4.1 29.2 - - + -
411 THR* 3.5 4.0 - - - +
421 VAL* 2.8 41.6 + - - +
1001 ILE 3.8 0.6 + - - -
1011 VAL* 1.3 75.6 - - - +
1031 GLY* 1.3 59.2 + - - +
1091 PHE 3.5 3.8 - - - -
1101 LEU* 3.6 18.2 - - + -
1781 ILE* 3.7 3.6 - - + +
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Residues in contact with GLY 103 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121 VAL* 3.5 11.0 - - - +
401 ASN 3.0 13.2 - - - -
761 PRO* 3.9 11.9 - - - -
1021 ALA* 1.3 76.8 - - - +
1041 VAL* 1.3 61.7 + - - +
1081 GLN* 3.5 2.8 - - - -
1091 PHE* 2.6 42.9 + - - +
1781 ILE* 4.0 3.6 - - - -
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Residues in contact with VAL 104 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111 GLY* 4.1 13.2 - - - -
121 VAL 4.8 0.4 - - - +
401 ASN* 3.0 29.5 + - + +
761 PRO* 3.7 5.7 - - - +
1031 GLY* 1.3 77.0 - - - +
1051 GLN* 1.3 76.1 + - - +
1061 GLY* 3.4 27.1 - - - +
1071 ASP 3.3 3.4 - - - +
1081 GLN* 4.8 2.5 - - - -
1781 ILE* 3.1 41.1 - - + +
1791 ASP 5.1 0.2 - - - -
1801 LYS* 3.9 21.1 - - + +
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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