Contacts of the strand formed by residues 54 - 72 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLU 4.4 0.8 + - - -
53A VAL* 1.3 71.4 - - - +
55A LEU* 1.3 62.7 + - - +
128A ASN* 3.4 1.7 - - - -
129A LEU* 2.7 53.3 + - + +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL 3.8 1.2 + - - -
54A ALA* 1.3 72.3 - - - +
56A LEU* 1.3 64.7 + - - +
57A ARG 4.3 8.1 - - - +
58A THR* 3.5 10.3 - - - +
126A THR* 3.4 25.4 - - - +
127A GLY 4.7 1.6 - - - +
128A ASN* 3.6 19.4 - - - +
129A LEU* 4.9 2.7 - - - +
222A ALA 4.4 5.9 - - - +
223A GLY* 3.5 27.8 - - - +
224A ALA* 3.8 21.8 - - + -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA 3.6 1.0 + - - -
55A LEU* 1.3 76.1 - - - +
57A ARG* 1.4 66.1 + - + +
127A GLY 3.2 13.8 + - - +
129A LEU* 3.8 32.5 - - + -
197A ILE* 3.8 26.9 - - + -
210A LYS* 4.9 6.5 - - - -
213A PHE* 4.9 7.6 - - + -
214A LEU* 3.9 32.1 - - + -
222A ALA* 3.7 17.2 - - - +
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 4.3 2.4 - - - +
56A LEU* 1.4 85.5 + - + +
58A THR* 1.3 66.1 + - - +
59A TYR* 2.9 36.1 + - + -
126A THR* 4.4 0.3 + - - -
127A GLY 3.1 26.3 + - - +
213A PHE* 3.4 21.2 - - + -
214A LEU* 3.3 38.9 + - - +
220A TRP* 3.6 53.6 - - + +
221A THR 3.6 14.6 - - - +
222A ALA* 5.3 0.4 - - - -
236A ARG* 5.6 0.6 - - - +
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Residues in contact with THR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.5 12.8 - - - +
57A ARG* 1.3 75.9 + - - +
59A TYR* 1.3 60.6 + - - +
124A LYS* 4.3 27.4 - - + -
125A ILE 3.4 19.7 - - - +
126A THR* 4.0 12.4 + - - -
220A TRP* 3.3 2.7 - - - -
221A THR* 3.0 47.0 + - - +
223A GLY 3.5 13.0 + - - -
224A ALA* 4.5 6.3 - - + +
231A TRP* 3.3 6.6 - - + -
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 2.9 42.9 + - - -
58A THR* 1.3 75.1 - - - +
60A CYS* 1.3 58.0 + - - +
61A ILE* 4.1 0.7 - - + -
124A LYS* 3.4 6.6 - - - +
125A ILE* 2.8 43.1 + - + +
213A PHE* 3.0 58.5 + + + -
214A LEU* 3.0 9.0 + - - -
216A LEU* 3.4 23.2 + - + -
218A LEU* 3.3 49.1 - - + -
219A PRO 3.4 1.8 - - - -
220A TRP* 3.7 13.9 - + + -
231A TRP* 3.8 2.7 - - - -
236A ARG* 5.1 0.2 + - - -
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Residues in contact with CYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 1.3 71.2 - - - +
61A ILE* 1.3 58.8 + - - +
62A GLU 3.4 16.4 - - - -
63A ALA* 4.2 1.6 - - - -
119A PHE* 4.1 15.0 - - - -
121A CYS* 2.0 51.6 - - - -
123A GLY 3.9 0.2 - - - -
218A LEU* 3.4 24.0 - - - +
219A PRO* 2.9 24.1 + - + +
231A TRP* 3.7 13.2 - - + -
237A MET* 3.4 8.3 - - - +
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 4.1 1.5 + - + +
60A CYS* 1.3 73.3 - - - +
62A GLU* 1.3 69.8 + - + +
123A GLY* 3.0 22.8 + - - +
125A ILE* 3.7 40.2 - - + -
201A MET* 4.5 2.2 - - + -
202A LYS* 5.5 5.6 - - - -
218A LEU* 3.9 24.0 - - + -
237A MET* 3.4 10.1 - - - +
254A GLY 3.3 6.4 - - - +
255A SER* 4.4 2.2 - - - +
256A GLN* 2.9 39.3 + - + +
257A GLU* 4.0 31.9 - - + +
260A MET* 4.5 13.2 - - + -
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A CYS* 3.4 9.5 - - - -
61A ILE* 1.3 80.9 - - + +
63A ALA* 1.3 65.9 + - - +
122A SER* 2.7 48.9 + - - +
123A GLY* 3.1 20.7 + - - +
202A LYS* 5.6 4.0 + - - -
254A GLY 3.7 5.4 - - - +
255A SER* 3.5 31.5 + - - +
257A GLU* 5.6 1.6 - - - +
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A CYS* 4.2 2.9 - - - -
62A GLU* 1.3 78.6 - - - +
64A SER* 1.3 62.4 + - - +
119A PHE* 3.8 33.2 - - + -
120A SER 3.4 12.3 - - - +
122A SER* 4.7 3.6 - - - +
237A MET* 3.8 16.0 - - + +
252A VAL* 3.4 21.2 - - + +
254A GLY* 3.8 9.5 + - - +
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ALA* 1.3 76.6 - - - +
65A ILE* 1.3 67.5 + - - +
66A SER* 4.9 1.8 + - - -
118A LYS 3.7 1.7 - - - +
119A PHE* 4.4 1.8 - - - -
120A SER* 2.8 55.4 + - - -
122A SER* 5.6 4.1 + - - -
252A VAL* 4.5 5.6 - - - -
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 1.3 75.2 - - - +
66A SER* 1.3 66.8 + - - +
68A ILE* 3.8 19.9 - - + +
91A ILE* 4.6 3.4 - - + -
117A ALA* 3.8 17.9 - - + -
118A LYS 3.7 15.5 - - - +
119A PHE* 4.8 4.0 - - + -
238A VAL* 3.8 35.0 - - + -
250A VAL* 3.7 31.9 - - + +
251A THR 5.3 0.9 - - - -
252A VAL* 3.7 26.2 - - + +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 4.8 1.7 + - - -
65A ILE* 1.3 78.7 + - - +
67A ASN* 1.4 75.7 + - - +
68A ILE* 3.7 3.5 + - - -
117A ALA* 3.7 2.8 - - - +
118A LYS* 2.8 48.5 + - - +
120A SER* 4.1 14.1 + - - -
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Residues in contact with ASN 67 (chain A).
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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66A SER* 1.4 85.6 - - - +
68A ILE* 1.3 64.4 + - - +
69A THR* 3.7 7.6 + - + +
90A TYR* 3.4 30.5 - - - +
116A CYS 3.5 9.7 - - - +
118A LYS* 4.3 7.0 + - - +
1001A NAG 1.5 63.9 + - - +
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.8 32.3 - - + +
66A SER* 4.9 1.6 - - - -
67A ASN* 1.3 75.4 - - - +
69A THR* 1.3 66.1 + - - +
70A THR* 4.3 7.5 + - - +
115A THR* 3.9 25.8 - - + -
116A CYS 3.5 6.1 - - - +
117A ALA* 4.3 3.8 - - + -
248A GLN 5.3 5.2 - - - +
250A VAL* 3.8 17.7 - - + -
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASN* 4.4 8.0 + - + +
68A ILE* 1.3 78.1 - - - +
70A THR* 1.3 61.3 + - - +
82A LEU* 3.8 17.6 - - + +
84A GLU* 2.8 30.9 + - - +
114A VAL 3.7 2.3 - - - +
115A THR* 3.6 3.5 - - - -
116A CYS* 2.9 41.3 + - - +
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Residues in contact with THR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 4.4 6.3 + - - +
69A THR* 1.3 74.2 - - - +
71A ALA* 1.3 62.1 + - - +
72A THR* 4.1 16.3 + - + +
82A LEU* 4.8 1.8 - - - -
113A VAL* 5.6 4.7 - - + -
114A VAL 3.6 4.7 - - - +
115A THR* 3.7 27.2 - - + +
248A GLN* 4.9 17.7 + - + -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A THR 4.2 0.4 - - - -
70A THR* 1.3 72.7 - - - +
72A THR* 1.3 61.3 + - - +
80A PRO* 3.6 22.0 - - + +
81A TYR 4.7 5.4 - - - +
82A LEU* 3.8 19.5 - - + -
113A VAL* 3.5 6.2 - - - +
114A VAL* 3.0 41.2 + - + -
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A THR* 4.1 15.1 + - + +
71A ALA* 1.3 77.4 - - - +
73A ARG* 1.3 70.7 + - - +
80A PRO* 4.8 0.2 - - - +
99A ARG* 3.5 22.4 + - - +
113A VAL* 3.8 18.8 - - + -
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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