Contacts of the strand formed by residues 54 - 72 (chain B) in PDB entry 3UAJ
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 ALA 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B GLU 4.4 0.4 - - - -
53B VAL* 1.3 71.5 - - - +
55B LEU* 1.3 63.1 + - - +
128B ASN* 4.1 1.3 - - - -
129B LEU* 2.8 53.0 + - + +
131B GLN* 4.4 6.8 - - - +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL 3.9 1.0 + - - -
54B ALA* 1.3 73.0 - - - +
56B LEU* 1.3 62.8 + - - +
57B ARG 4.0 6.5 - - - +
58B THR* 3.4 26.9 - - - +
126B THR* 3.8 24.5 - - + -
127B GLY 3.8 10.3 - - - +
128B ASN* 3.9 13.4 - - - +
222B ALA 5.0 14.7 - - - +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA 3.6 0.8 + - - -
55B LEU* 1.3 74.6 - - - +
57B ARG* 1.4 67.8 + - + +
127B GLY 3.3 12.2 + - - +
129B LEU* 4.8 19.3 - - + -
197B ILE* 3.8 29.2 - - + -
210B LYS* 4.9 8.5 - - - -
213B PHE* 5.0 5.4 - - + -
214B LEU* 3.9 33.2 - - + -
222B ALA* 3.7 17.7 - - - +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 4.0 2.1 - - - +
56B LEU* 1.4 86.6 + - + +
58B THR* 1.3 66.9 + - - +
59B TYR* 2.9 36.2 + - + -
127B GLY 3.3 25.3 + - - +
213B PHE* 3.5 21.7 - - + -
214B LEU* 3.3 39.0 + - + +
220B TRP* 3.6 54.3 - - + +
221B THR 3.6 14.1 - - - +
222B ALA* 5.1 1.1 - - - -
236B ARG* 5.5 0.4 - - - +
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.4 25.8 - - - +
57B ARG* 1.3 75.4 + - - +
59B TYR* 1.3 64.5 + - - +
124B LYS* 4.4 21.3 - - + -
125B ILE 3.4 19.7 - - - +
126B THR* 4.5 9.5 - - - +
220B TRP* 3.3 0.8 - - - -
221B THR* 3.0 47.8 + - - +
231B TRP* 3.3 8.5 - - + -
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Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ARG* 2.9 42.3 + - - -
58B THR* 1.3 74.8 - - - +
60B CYS* 1.3 57.6 + - - +
124B LYS* 3.4 8.0 - - - +
125B ILE* 2.9 45.8 + - + +
213B PHE* 2.9 58.2 + + - -
214B LEU* 3.0 9.7 + - - -
216B LEU* 3.5 19.7 - - + -
218B LEU* 3.3 45.8 - - + -
219B PRO 3.4 5.2 - - - -
220B TRP* 3.7 14.8 - + + -
231B TRP* 3.7 2.5 - - - -
236B ARG* 4.5 0.2 - - - -
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Residues in contact with CYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR* 1.3 72.8 - - - +
61B ILE* 1.3 59.3 + - - +
62B GLU 3.4 15.5 - - - -
63B ALA* 4.2 2.0 - - - -
119B PHE* 4.1 14.6 - - - -
121B CYS* 2.0 52.5 - - - -
123B GLY 3.9 0.4 - - - -
218B LEU* 3.4 24.3 - - - +
219B PRO* 2.9 19.8 + - + +
231B TRP* 3.7 16.8 - - + -
237B MET* 3.4 8.5 - - - +
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR 4.2 0.6 - - - -
60B CYS* 1.3 73.9 - - - +
62B GLU* 1.3 69.7 + - + +
123B GLY* 3.0 23.9 + - - +
124B LYS* 4.5 7.6 - - - +
125B ILE* 4.1 18.6 - - + +
201B MET* 4.0 21.3 - - + -
218B LEU* 3.9 24.2 - - + -
237B MET* 3.4 9.8 - - - +
254B GLY 3.3 6.6 - - - +
255B SER* 4.4 2.0 - - - +
256B GLN* 2.9 40.1 + - + +
257B GLU* 4.1 23.6 - - + +
260B MET* 4.5 14.8 - - + -
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B CYS* 3.4 9.2 - - - -
61B ILE* 1.3 81.4 - - + +
63B ALA* 1.3 64.4 + - - +
122B SER* 2.7 48.8 + - - +
123B GLY* 3.1 20.0 + - - +
254B GLY 3.7 5.2 - - - +
255B SER* 3.5 30.8 + - - +
257B GLU* 5.6 1.2 - - - +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B CYS* 4.2 2.0 - - - -
62B GLU* 1.3 77.3 - - - +
64B SER* 1.3 63.0 + - - +
119B PHE* 3.8 34.5 - - + -
120B SER 3.4 11.9 - - - +
122B SER* 4.7 3.8 - - - +
237B MET* 3.8 15.8 - - + +
252B VAL* 3.4 20.1 - - + +
254B GLY* 3.8 10.8 + - - +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ALA* 1.3 76.5 - - - +
65B ILE* 1.3 65.8 + - - +
66B SER* 4.9 1.8 + - - -
118B LYS 3.7 1.9 - - - +
119B PHE* 4.4 2.3 - - - -
120B SER* 2.8 56.3 + - - -
122B SER* 5.7 4.1 + - - -
252B VAL* 4.3 6.5 - - - +
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B SER* 1.3 74.3 - - - +
66B SER* 1.3 66.3 + - - +
68B ILE* 3.9 24.7 - - + -
91B ILE* 6.1 0.4 - - + -
117B ALA* 4.6 12.6 - - + -
118B LYS 3.7 4.7 - - - +
119B PHE* 6.1 1.6 - - + -
238B VAL* 4.6 20.2 - - + -
250B VAL* 4.0 37.5 - - + +
251B THR 5.3 0.2 - - - -
252B VAL* 3.8 26.7 - - + +
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Residues in contact with SER 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B SER* 4.8 1.6 + - - -
65B ILE* 1.3 77.6 + - - +
67B ASN* 1.4 74.9 + - - +
68B ILE* 3.7 5.3 + - - -
117B ALA* 3.7 2.8 - - - +
118B LYS* 2.8 47.3 + - - +
120B SER* 4.2 13.5 + - - -
1001B NAG 5.5 1.3 - - - -
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Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B SER* 1.4 84.7 - - - +
68B ILE* 1.3 64.4 + - - +
69B THR* 3.7 7.9 + - + +
90B TYR* 3.5 29.6 - - - +
116B CYS 3.5 3.5 - - - +
118B LYS* 3.8 14.7 + - - +
1001B NAG 1.4 72.2 + - - +
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 3.9 23.3 - - + -
66B SER* 4.5 3.1 - - - +
67B ASN* 1.3 77.4 - - - +
69B THR* 1.3 64.8 + - - +
70B THR* 4.3 7.3 + - - +
115B THR* 3.9 26.5 - - + -
116B CYS 3.5 6.1 - - - +
117B ALA* 4.3 9.6 - - + -
249B ASP* 6.6 0.4 - - - -
250B VAL* 3.8 26.0 - - + -
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Residues in contact with THR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ASN* 3.7 8.9 + - + +
68B ILE* 1.3 78.6 - - - +
70B THR* 1.3 62.4 + - - +
82B LEU* 3.8 15.8 - - + +
84B GLU* 2.8 32.2 + - - +
114B VAL 3.8 2.3 - - - +
115B THR* 3.6 2.9 - - - -
116B CYS* 2.9 41.7 + - - +
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ILE* 4.4 6.1 + - - +
69B THR* 1.3 76.0 + - - +
71B ALA* 1.3 62.8 + - - +
72B THR* 4.1 16.4 + - + +
82B LEU* 4.9 1.3 - - - -
113B VAL* 5.6 4.7 - - + -
114B VAL 3.6 4.0 - - - +
115B THR* 3.7 26.6 - - + +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B THR 4.2 0.4 - - - -
70B THR* 1.3 72.3 - - - +
72B THR* 1.3 61.2 + - - +
80B PRO* 3.6 21.7 - - + +
81B TYR 4.9 4.9 - - - +
82B LEU* 3.8 20.0 - - + -
113B VAL* 3.5 6.4 - - - +
114B VAL* 3.0 41.9 + - + -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B THR* 4.1 14.4 + - + +
71B ALA* 1.3 77.2 - - - +
73B ARG* 1.3 71.9 + - - +
80B PRO* 4.8 0.3 - - - +
99B ARG* 3.5 22.3 + - - +
113B VAL* 3.8 19.5 - - + -
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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