Contacts of the strand formed by residues 125 - 134 (chain T) in PDB entry 6O81
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 LYS 125 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89T TYR* 3.4 3.5 - - - -
90T LYS* 2.8 35.9 + - - +
91T LEU* 5.0 2.2 - - - +
124T PHE* 1.3 74.5 - - - +
126T LEU* 1.3 62.2 + - - +
127T VAL* 4.1 1.4 + - - +
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Residues in contact with LEU 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T VAL* 4.3 11.6 - - - +
38T ARG* 5.5 12.9 - - + +
87T LYS* 4.9 17.0 - - + -
88T ILE 4.5 2.7 - - - +
89T TYR* 4.1 17.2 - - + +
124T PHE 4.3 0.6 + - - -
125T LYS* 1.3 74.2 - - - +
127T VAL* 1.3 61.2 + - - +
128T ARG 5.4 1.8 - - - +
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Residues in contact with VAL 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T HIS 4.5 5.4 - - - +
34T GLU 4.1 6.1 - - - +
35T VAL* 3.8 27.2 + - + +
38T ARG* 5.4 6.4 - - - +
41T THR* 5.5 0.3 - - - -
88T ILE 4.4 4.8 + - - +
125T LYS 4.1 2.1 + - - +
126T LEU* 1.3 76.0 - - - +
128T ARG* 1.3 64.3 + - + +
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Residues in contact with ARG 128 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T HIS* 5.2 13.0 - - + -
38T ARG* 6.5 0.2 - - - +
41T THR* 4.3 15.3 - - - -
42T ILE* 6.4 0.7 - - + -
87T LYS* 4.7 0.8 - - - -
88T ILE* 3.6 26.2 + - - +
126T LEU* 5.7 2.0 - - - +
127T VAL* 1.3 81.3 + - + +
129T HIS* 1.3 62.5 + - - +
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Residues in contact with HIS 129 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T ARG* 5.0 10.8 - - - +
39T GLN 4.2 21.5 - - - +
40T ALA* 4.9 0.4 - - - -
41T THR* 3.4 14.2 + - - +
42T ILE* 3.2 27.4 + - - +
85T ASN* 5.8 1.8 - - + -
86T ALA 3.2 19.5 - - - +
87T LYS* 4.2 8.7 - - + +
128T ARG* 1.3 76.5 - - - +
130T VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 130 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42T ILE* 3.5 7.6 - - + +
44T ILE* 4.9 12.6 - - + -
84T ALA 3.6 2.1 - - - +
85T ASN* 4.6 1.1 - - - -
86T ALA* 2.9 40.7 + - + +
88T ILE* 6.0 3.1 - - + +
128T ARG 4.5 0.2 + - - -
129T HIS* 1.3 73.7 - - - +
131T SER* 1.3 62.0 + - - +
132T PHE* 3.7 1.9 + - + +
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Residues in contact with SER 131 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40T ALA* 5.6 2.9 - - - -
42T ILE 2.9 11.5 + - - -
43T ASN* 3.5 5.7 - - - +
44T ILE* 2.9 26.2 + - - +
83T TYR* 4.9 12.5 - - - -
84T ALA 3.5 8.1 - - - -
85T ASN* 4.4 7.0 - - - +
130T VAL* 1.3 70.3 - - - +
132T PHE* 1.3 65.5 + - - +
133T VAL* 3.5 2.4 + - - +
334T GLY 3.5 24.9 - - - -
335T GLY* 4.1 13.0 - - - -
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Residues in contact with PHE 132 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T ILE* 3.3 11.7 - - + +
46T THR* 5.6 7.0 - - - -
58T VAL* 5.0 13.0 - - + -
82T GLY 3.4 2.1 - - - +
83T TYR* 3.4 3.2 - - - -
84T ALA* 2.9 41.9 + - + +
86T ALA* 6.3 1.8 - - + -
130T VAL* 3.7 3.9 + - + +
131T SER* 1.3 70.7 - - - +
133T VAL* 1.3 60.0 + - - +
134T ASP* 3.7 3.2 + - + +
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Residues in contact with VAL 133 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43T ASN* 6.0 2.7 - - + -
44T ILE 2.9 16.3 + - - +
45T GLY* 4.0 6.8 - - - -
46T THR* 3.3 27.4 + - - +
81T LEU* 5.3 5.8 - - + -
82T GLY 3.5 5.4 - - - -
83T TYR* 3.7 28.3 - - + -
131T SER 3.5 2.0 + - - +
132T PHE* 1.3 70.7 - - - +
134T ASP* 1.3 60.3 + - - +
135T CYS* 4.0 1.7 + - - +
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Residues in contact with ASP 134 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46T THR* 4.6 8.7 - - - +
54T LYS* 5.1 19.7 - - + +
55T SER* 5.6 5.2 - - - +
58T VAL* 5.8 5.6 - - + -
80T LYS 4.8 0.2 - - - +
81T LEU* 3.5 1.0 - - - -
82T GLY* 2.9 35.7 + - - +
132T PHE* 3.7 3.5 + - + +
133T VAL* 1.3 72.5 - - - +
135T CYS* 1.3 60.8 + - - +
136T PRO 4.3 0.3 - - - -
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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