Contacts of the strand formed by residues 1037 - 1043 (chain K) in PDB entry 6R90
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 ILE1037 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8K THR* 3.7 4.9 - - - +
9K ALA* 2.9 29.6 + - + -
10K GLN* 2.9 27.5 + - + +
356K LEU* 3.7 23.1 - - + -
359K ILE* 3.9 13.0 - - + -
362K MET* 5.2 1.6 - - + -
375K LEU* 4.6 17.0 - - + -
390K ILE* 3.8 26.9 - - + -
710K LEU* 6.1 0.2 - - + -
1012K LEU* 5.7 6.1 - - + -
1029K LEU* 4.5 15.5 - - + -
1030K PHE 3.5 11.4 - - - +
1031K GLY* 5.2 0.9 - - - -
1035K GLY 3.8 6.5 - - - +
1036K MET* 1.3 81.7 - - - +
1038K GLY* 1.3 68.1 + - - +
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Residues in contact with GLY1038 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K VAL 3.4 10.8 - - - -
8K THR* 4.4 2.0 - - - -
9K ALA* 4.3 2.2 - - - -
1029K LEU* 3.3 11.6 - - - +
1030K PHE* 2.9 57.7 + - - -
1036K MET* 5.6 1.8 - - - -
1037K ILE* 1.3 75.2 - - - +
1039K LEU* 1.3 59.9 + - - -
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Residues in contact with LEU1039 (chain K).
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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5K TYR 3.9 0.3 - - - +
6K VAL* 3.2 6.8 - - - +
7K VAL* 2.9 40.5 + - + +
9K ALA* 5.6 0.9 - - + -
1010K GLY 4.9 0.4 - - - +
1011K SER* 5.7 2.7 - - - +
1027K SER* 3.9 15.7 - - - -
1028K VAL 3.1 39.3 - - - +
1029K LEU* 3.9 18.2 - - + +
1030K PHE* 3.7 0.6 - - - -
1038K GLY* 1.3 74.9 - - - -
1040K VAL* 1.3 69.5 - - - +
1041K THR* 5.1 6.1 - - + -
1139K ILE* 3.5 45.3 - - + +
1140K HIS* 4.5 9.0 - - + -
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Residues in contact with VAL1040 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K ASN* 4.4 9.0 - - + -
5K TYR 3.5 3.6 - - - -
6K VAL* 3.7 24.2 - - + -
960K LEU* 4.4 19.1 - - + -
966K LEU* 4.5 18.6 - - + -
974K LEU* 4.8 5.4 - - + -
1007K PHE* 4.8 1.3 - - + -
1027K SER* 3.8 0.5 + - - -
1028K VAL* 2.8 44.3 + - + +
1030K PHE* 3.4 32.1 - - + -
1039K LEU* 1.3 76.4 - - - +
1041K THR* 1.3 70.8 + - - +
1088K PHE* 4.5 5.6 - - + -
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Residues in contact with THR1041 (chain K).
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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4K ASN* 3.0 13.1 - - - +
5K TYR* 2.9 52.3 + - + +
960K LEU* 5.7 1.8 - - - -
1024K THR* 3.4 29.5 - - + -
1025K GLN 2.5 31.1 + - - -
1026K GLY 2.6 18.6 + - - -
1027K SER* 4.9 0.7 - - - -
1039K LEU* 5.1 6.7 - - + -
1040K VAL* 1.3 76.0 - - - +
1042K SER* 1.3 59.0 + - - +
1139K ILE* 5.1 3.6 - - + -
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Residues in contact with SER1042 (chain K).
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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2K SER* 5.7 0.2 + - - -
3K TYR 3.6 1.8 - - - -
4K ASN* 3.2 16.7 + - - -
960K LEU* 4.2 18.9 + - - +
961K ASP* 4.9 7.4 + - - -
964K ASN* 5.7 1.6 + - - +
1024K THR* 3.5 6.1 - - - -
1025K GLN* 2.7 57.4 + - - +
1041K THR* 1.3 75.6 - - - +
1043K LEU* 1.3 58.9 + - - +
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Residues in contact with LEU1043 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K TYR* 2.6 37.4 + - + +
4K ASN* 4.4 4.5 - - - +
5K TYR* 4.8 10.3 - - + +
1023K PRO* 3.0 36.6 - - + +
1024K THR* 4.8 4.0 - - + -
1025K GLN* 3.2 5.4 - - - -
1042K SER* 1.3 76.8 - - - +
1044K SER* 1.3 67.6 + - - +
1047K TRP* 3.2 28.9 - - + -
1048K TYR* 3.3 31.6 - - + +
1051K LEU* 3.8 18.4 - - + -
1089K ILE* 4.6 9.0 - - + -
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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