Contacts of the strand formed by residues 54 - 67 (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 GLY 54 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52T SER 3.6 1.4 + - - -
53T GLU* 1.3 89.4 - - - +
55T LEU* 1.3 60.8 + - - -
56T TYR* 3.5 11.4 - - - -
125T GLN* 3.4 8.9 - - - -
126T LEU 2.9 31.8 + - - +
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Residues in contact with LEU 55 (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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54T GLY* 1.3 72.5 - - - -
56T TYR* 1.3 64.5 + - - +
123T VAL* 4.3 10.1 - - + -
124T PHE 3.4 4.0 - - - +
125T GLN* 3.8 33.0 - - + +
156T ALA* 3.6 1.9 - - - +
157T LEU* 2.8 55.5 + - + +
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Residues in contact with TYR 56 (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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12T PRO* 4.0 13.3 - - + +
50T VAL* 3.4 18.4 - - + +
51T PRO* 3.7 8.5 - - + +
52T SER* 2.6 41.3 + - - -
54T GLY* 3.5 20.0 - - - -
55T LEU* 1.3 78.8 - - - +
57T LEU* 1.3 61.8 + - - +
58T ILE* 3.5 12.7 + - + +
122T GLY 3.6 0.2 - - - +
123T VAL* 3.3 5.3 - - - -
124T PHE 2.8 33.9 + - - +
126T LEU* 3.7 26.9 - - + -
154T ILE* 3.9 24.9 - - + -
155T ILE 3.4 7.0 - - - +
156T ALA* 3.5 33.6 - - + +
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Residues in contact with LEU 57 (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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56T TYR* 1.3 70.3 - - - +
58T ILE* 1.3 62.3 + - - +
59T TYR* 4.6 12.0 - - + -
121T GLY* 4.7 2.2 - - - -
122T GLY* 3.5 31.0 - - - +
123T VAL* 4.2 13.7 - - + +
154T ILE* 3.1 5.2 - - - +
155T ILE* 2.8 65.1 + - + +
157T LEU* 4.0 18.2 - - + +
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Residues in contact with ILE 58 (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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56T TYR* 3.8 20.9 - - + +
57T LEU* 1.3 81.6 - - - +
59T TYR* 1.3 62.4 + - - +
80T ILE* 3.7 22.2 - - + -
93T LEU* 3.5 23.1 - - + -
94T LEU* 3.6 12.3 - - + -
121T GLY* 3.1 2.9 - - - -
122T GLY 2.8 42.6 + - - +
124T PHE* 3.5 24.2 - - + -
126T LEU* 4.2 4.9 - - + -
132T LEU* 4.0 12.8 - - + -
152T PHE* 5.5 1.1 - - + -
153T GLY 3.5 4.3 - - - -
154T ILE* 3.9 21.1 - - + -
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Residues in contact with TYR 59 (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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14T ALA 3.9 2.0 + - - -
15T HIS* 2.6 41.3 + + - +
57T LEU* 4.6 16.4 - - + -
58T ILE* 1.3 80.2 - - - +
60T SER* 1.3 65.2 + - - +
80T ILE* 3.7 6.1 - - - +
119T TYR* 3.5 25.8 - - + +
120T LEU 3.1 13.2 - - - +
121T GLY* 4.0 3.1 - - - -
151T TYR* 3.7 22.7 - + - -
152T PHE* 3.4 4.3 - - - -
153T GLY* 2.9 58.0 + - - +
154T ILE 4.0 2.2 - - - -
155T ILE* 4.5 17.7 - - + +
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Residues in contact with SER 60 (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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28T TRP* 4.1 3.3 - - - -
59T TYR* 1.3 80.3 - - - +
61T GLN* 1.3 60.7 + - - +
78T HIS* 3.0 29.6 + - - -
80T ILE* 3.6 18.4 - - - +
119T TYR* 3.5 4.1 - - - -
120T LEU 3.0 30.5 + - - +
134T ALA* 3.8 8.9 - - - +
151T TYR* 2.8 24.5 + - - -
152T PHE* 4.1 7.8 - - - +
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Residues in contact with GLN 61 (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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60T SER* 1.3 74.7 - - - +
62T VAL* 1.3 75.6 + - - +
63T LEU* 4.7 6.5 - - - +
117T PRO* 5.1 10.1 - - + +
118T ILE 3.3 15.3 - - - +
119T TYR* 4.0 9.8 - - + +
148T GLY 3.7 5.1 + - - -
149T GLN* 2.7 32.6 + - - +
150T VAL* 3.3 2.8 - - - -
151T TYR* 2.7 74.4 + - + +
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Residues in contact with VAL 62 (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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26T LEU* 4.6 7.0 - - + -
28T TRP* 4.9 1.3 - - + -
60T SER* 4.5 1.8 - - - +
61T GLN* 1.3 81.7 - - - +
63T LEU* 1.3 58.8 + - - +
64T PHE* 3.5 30.5 - - + -
78T HIS* 3.5 42.5 - - + +
116T GLU 4.1 0.2 - - - +
117T PRO* 3.3 2.4 - - - +
118T ILE* 2.9 33.7 + - + +
136T ILE* 3.7 11.9 - - + -
142T LEU* 3.8 12.6 - - + -
149T GLN 3.8 4.7 - - - -
150T VAL* 4.0 15.9 - - + -
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Residues in contact with LEU 63 (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* 4.7 4.3 - - - +
62T VAL* 1.3 73.6 - - - +
64T PHE* 1.3 67.9 + - - +
115T TYR* 4.4 15.5 - - + -
116T GLU 3.7 5.4 - - - +
117T PRO* 3.8 31.6 - - + -
142T LEU* 3.6 5.5 - - - +
143T ASP* 2.8 47.3 + - + +
149T GLN* 3.5 54.6 + - + +
150T VAL* 4.0 3.6 - - - +
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Residues in contact with PHE 64 (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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62T VAL* 3.5 20.4 - - + -
63T LEU* 1.3 76.2 - - - +
65T LYS* 1.3 60.0 + - - +
76T LEU* 3.7 44.2 - - + -
77T THR 3.8 12.1 - - - -
114T TRP* 3.9 6.5 - - + -
115T TYR* 3.3 7.6 - - - +
116T GLU* 2.8 44.1 + - + +
118T ILE* 4.1 15.0 - - + -
136T ILE* 3.6 35.9 - - + -
137T ASN* 4.7 0.2 - - - -
138T ARG* 3.5 32.5 - - + -
141T TYR* 3.3 16.6 - - + +
142T LEU* 4.3 3.8 - - + -
143T ASP* 4.5 0.4 - - - -
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Residues in contact with LYS 65 (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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118C TRP* 3.4 56.8 - - + +
64T PHE* 1.3 73.9 - - - +
66T GLY* 1.3 65.6 + - - +
113T PRO* 5.8 2.2 - - + -
114T TRP* 3.3 13.9 - - - +
115T TYR* 3.4 38.0 + - + +
141T TYR* 2.8 29.5 + - - +
143T ASP* 3.7 29.4 + - + +
145T ALA* 6.1 1.6 - - - +
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Residues in contact with GLY 66 (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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118C TRP* 3.5 12.8 - - - -
65T LYS* 1.3 78.5 - - - +
67T GLN* 1.3 60.8 + - - -
113T PRO* 3.3 5.7 - - - +
114T TRP* 2.8 58.7 + - - +
141T TYR* 3.9 1.3 - - - -
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Residues in contact with GLN 67 (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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115C ASN* 4.9 5.0 + - - +
118C TRP* 2.9 39.1 + - + +
119C SER* 3.3 24.7 + - - +
122C PHE* 3.7 3.5 - - - -
124C VAL* 3.8 20.7 - - + +
128C GLY* 3.6 28.3 - - - -
66T GLY* 1.3 72.3 - - - -
68T GLY* 1.3 64.5 + - - +
111T ALA* 3.3 25.8 + - + +
112T LYS 4.1 2.2 - - - -
113T PRO* 4.3 6.8 - - + +
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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