Contacts of the strand formed by residues 113 - 126 (chain T) in PDB entry 3L9J
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 PRO 113 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65T LYS* 5.8 2.2 - - + -
66T GLY 3.3 11.2 - - - +
67T GLN* 4.3 5.8 - - + +
110T GLU* 5.7 4.3 - - + +
111T ALA 3.5 7.2 - - - +
112T LYS* 1.3 95.0 - - + +
114T TRP* 1.3 60.8 + - - +
115T TYR* 4.4 21.0 - - + +
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Residues in contact with TRP 114 (chain T).
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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64T PHE* 3.9 22.0 - - + -
65T LYS* 3.3 6.3 - - - +
66T GLY* 2.8 55.4 + - - +
68T GLY 3.0 30.3 + - - -
69T CYS* 4.0 15.3 - - - -
76T LEU* 3.9 7.0 - - + -
100T PRO* 3.5 48.2 - - + +
101T CYS* 3.6 7.8 - - - -
112T LYS 4.2 2.5 - - - +
113T PRO* 1.3 74.4 - - - +
115T TYR* 1.3 73.2 + - - +
116T GLU* 3.9 8.7 - - + +
141T TYR* 3.7 42.6 - + + -
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Residues in contact with TYR 115 (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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63T LEU* 4.4 19.1 - - + -
64T PHE 3.3 8.1 - - - -
65T LYS* 3.4 34.3 + - + +
113T PRO* 4.4 19.6 - - + +
114T TRP* 1.3 82.2 - - - +
116T GLU* 1.3 75.0 + - - +
117T PRO* 4.1 5.7 - - + +
143T ASP* 3.4 24.1 + - - -
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Residues in contact with GLU 116 (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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63T LEU* 3.7 1.3 - - - +
64T PHE* 2.8 44.4 + - + +
76T LEU* 4.1 14.1 - - + -
98T LYS* 2.6 48.3 + - + -
99T SER 4.6 2.5 - - - +
100T PRO* 3.8 40.0 - - + +
114T TRP* 3.9 6.2 - - + +
115T TYR* 1.3 81.2 - - - +
117T PRO* 1.3 66.2 - - - +
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Residues in contact with PRO 117 (chain T).
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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61T GLN* 5.1 11.9 - - - +
62T VAL 3.3 9.4 - - - +
63T LEU* 3.8 18.4 - - + -
98T LYS* 2.8 33.9 + - - +
115T TYR* 4.1 6.3 - - + +
116T GLU* 1.3 87.8 - - - +
118T ILE* 1.3 60.6 + - - +
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Residues in contact with ILE 118 (chain T).
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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61T GLN* 3.3 8.2 - - - +
62T VAL* 2.9 31.8 + - + +
64T PHE* 4.1 20.4 - - + -
76T LEU 4.3 6.7 - - - +
78T HIS* 3.7 37.1 + - + +
96T ALA* 3.7 38.8 - - + +
97T ILE 4.5 0.2 - - - +
98T LYS* 3.8 32.8 - - + +
117T PRO* 1.3 80.0 - - - +
119T TYR* 1.3 62.7 + - - +
120T LEU* 4.2 6.1 - - + -
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Residues in contact with TYR 119 (chain T).
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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59T TYR* 3.5 26.5 - + + +
60T SER 3.5 7.9 - - - -
61T GLN* 4.0 8.1 - - + +
117T PRO 4.3 0.2 - - - -
118T ILE* 1.3 75.4 - - - +
120T LEU* 1.3 84.0 + - - +
121T GLY* 4.2 6.7 - - - -
151T TYR* 3.4 35.8 - + - -
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Residues in contact with LEU 120 (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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59T TYR* 3.1 5.8 - - - +
60T SER 3.0 32.3 + - - +
78T HIS* 3.6 41.3 - - + +
79T THR* 4.0 0.2 - - - -
80T ILE* 3.8 19.5 - - + +
94T LEU* 3.7 35.4 - - + +
95T SER 3.8 29.2 - - - +
96T ALA* 3.9 13.0 - - + +
118T ILE* 4.2 2.5 - - + -
119T TYR* 1.3 85.9 - - - +
121T GLY* 1.3 59.7 - - - +
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Residues in contact with GLY 121 (chain T).
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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57T LEU* 4.7 4.9 - - - -
58T ILE 3.1 11.7 - - - -
59T TYR* 4.0 5.4 - - - -
94T LEU* 3.8 14.2 - - - +
119T TYR* 4.2 8.9 - - - -
120T LEU* 1.3 74.8 - - - +
122T GLY* 1.3 59.0 + - - -
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Residues in contact with GLY 122 (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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57T LEU* 3.5 7.7 - - - +
58T ILE* 2.8 39.7 + - - +
94T LEU* 3.8 5.0 - - - +
121T GLY* 1.3 74.8 - - - -
123T VAL* 1.3 61.3 + - - -
124T PHE* 3.6 16.1 - - - -
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Residues in contact with VAL 123 (chain T).
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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55T LEU* 4.3 19.1 - - + -
56T TYR 3.3 7.0 - - - +
57T LEU* 4.2 14.8 - - + -
122T GLY* 1.3 70.8 - - - -
124T PHE* 1.3 75.6 + - - +
157T LEU* 3.4 33.9 - - + -
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Residues in contact with PHE 124 (chain T).
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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55T LEU* 3.4 6.2 - - - -
56T TYR* 2.8 39.3 + - - +
58T ILE* 3.5 28.5 - - + -
93T LEU* 3.5 51.1 - - + -
94T LEU* 3.7 15.9 - - + -
122T GLY* 3.6 22.9 - - - -
123T VAL* 1.3 78.8 - - - +
125T GLN* 1.3 62.0 + - - +
126T LEU* 3.7 23.4 + - + +
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Residues in contact with GLN 125 (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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53T GLU* 2.8 42.8 + - - +
54T GLY* 3.4 16.7 - - - +
55T LEU* 3.8 20.5 + - + +
82T ARG* 3.6 17.8 + - - +
124T PHE* 1.3 71.8 - - - +
126T LEU* 1.3 73.5 + - - +
127T GLU* 3.9 10.2 + - - +
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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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50T VAL* 3.8 26.9 - - + -
53T GLU* 3.2 2.2 - - - -
54T GLY 2.9 30.2 + - - -
56T TYR* 3.7 37.0 - - + -
58T ILE* 4.2 5.4 - - + -
82T ARG* 3.8 25.1 - - + +
93T LEU* 4.4 2.5 - - + -
124T PHE* 4.0 20.6 - - + +
125T GLN* 1.3 89.1 + - - +
127T GLU* 1.3 64.9 + - - +
130T ASP* 3.7 5.8 - - + +
132T LEU* 3.9 28.3 - - + -
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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