Contacts of the strand formed by residues 109 - 129 (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 GLY 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PRO* 3.4 14.2 - - - +
99A ARG 2.9 31.1 + - - +
108A PHE* 1.3 75.2 - - - +
110A LYS* 1.3 63.7 + - - -
5B GLY 5.7 0.2 + - - -
316B GLN* 3.7 27.2 + - - +
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Residues in contact with LYS 110 (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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75A PRO* 4.3 10.2 - - - +
96A VAL* 4.1 37.0 - - + +
97A VAL 3.4 9.6 - - - +
98A ASP* 4.8 4.0 - - - +
109A GLY* 1.3 68.6 - - - -
111A GLY* 1.3 58.8 + - - +
112A GLY 4.2 1.0 + - - -
316B GLN* 4.2 17.0 - - - +
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Residues in contact with GLY 111 (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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73A ARG 3.4 16.4 - - - -
74A CYS 4.6 1.1 - - - -
75A PRO* 4.5 7.6 - - - -
96A VAL* 3.4 3.0 - - - -
97A VAL* 2.8 43.6 + - - +
99A ARG* 3.8 9.6 - - - -
109A GLY 3.4 3.4 + - - -
110A LYS* 1.3 72.2 - - - +
112A GLY* 1.3 65.0 + - - -
113A VAL* 3.7 0.6 + - - -
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 3.2 31.2 + - - +
74A CYS 5.3 0.8 + - - -
79A GLU* 5.2 9.2 - - - -
80A PRO* 3.4 22.2 - - - +
95A ASP 3.7 7.2 - - - -
96A VAL* 3.8 10.9 - - - +
110A LYS 4.2 0.8 + - - -
111A GLY* 1.3 70.9 - - - -
113A VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A THR* 5.6 5.6 - - + -
71A ALA 3.5 4.7 - - - +
72A THR* 3.8 30.7 - - + -
80A PRO* 3.9 2.6 - - - +
93A ARG 4.0 0.5 - - - +
94A ARG* 3.7 2.8 + - - +
95A ASP* 2.9 54.7 + - + +
97A VAL* 3.8 41.1 - - + -
99A ARG* 4.4 3.1 - - - +
111A GLY 4.3 0.7 - - - +
112A GLY* 1.3 78.1 - - - +
114A VAL* 1.3 63.0 + - - +
115A THR* 5.4 2.2 - - - +
242A VAL 5.9 1.1 - - - +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A THR 3.7 2.1 - - - +
70A THR* 3.6 3.0 - - - +
71A ALA* 3.0 43.7 + - + -
80A PRO* 3.6 32.8 - - + +
82A LEU* 3.8 11.4 - - + +
85A GLU* 3.7 25.4 - - - +
92A CYS* 4.5 1.3 - - + -
93A ARG 3.5 18.2 - - - +
94A ARG* 3.9 14.4 - - + -
113A VAL* 1.3 74.7 - - - +
115A THR* 1.3 64.0 + - - +
116A CYS* 4.4 11.7 - - - -
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Residues in contact with THR 115 (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* 3.9 24.9 - - + -
69A THR 3.6 5.2 - - - +
70A THR* 3.7 16.9 - - + +
92A CYS* 3.3 3.6 - - - -
93A ARG 3.3 30.2 + - - -
113A VAL* 5.4 2.8 - - - +
114A VAL* 1.3 73.3 + - - +
116A CYS* 1.3 64.8 + - - +
240A PHE* 3.4 28.8 - - + -
248A GLN 3.5 28.6 + - - +
250A VAL* 4.6 6.1 - - + -
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Residues in contact with CYS 116 (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 3.5 3.6 - - - +
68A ILE* 3.5 3.1 - - - -
69A THR* 2.9 47.6 + - - +
82A LEU* 3.9 18.2 - - + -
84A GLU* 3.9 17.5 - - + -
85A GLU* 3.9 10.5 - - - -
90A TYR* 4.1 3.1 - - + -
91A ILE 3.4 3.4 - - - -
92A CYS* 2.0 46.4 - - - -
114A VAL* 4.4 2.5 - - - -
115A THR* 1.3 74.2 - - - +
117A ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 117 (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 35.7 - - + -
66A SER 3.9 4.3 - - - +
67A ASN 3.9 1.6 - - - -
68A ILE* 4.3 9.0 - - + -
90A TYR* 3.4 5.7 - - - -
91A ILE* 2.9 40.2 + - + +
115A THR 4.4 0.2 - - - -
116A CYS* 1.3 73.7 - - - +
118A LYS* 1.3 62.7 + - - +
240A PHE* 5.4 0.2 - - + -
250A VAL* 4.4 15.3 - - + -
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Residues in contact with LYS 118 (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 3.7 6.1 - - - +
65A ILE* 3.7 5.4 - - - +
66A SER* 2.8 48.0 + - - +
67A ASN* 4.3 11.1 + - - +
89A GLN* 3.5 40.6 + - - +
90A TYR* 3.4 41.9 - - + +
117A ALA* 1.3 70.6 - - - +
119A PHE* 1.3 62.8 + - - +
120A SER* 3.9 4.2 + - - -
1001A NAG 4.6 16.3 + - - +
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Residues in contact with PHE 119 (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* 4.1 13.2 - - - -
63A ALA* 3.8 28.7 - - + -
64A SER 4.4 1.8 - - - -
65A ILE* 4.8 3.8 - - + -
89A GLN* 3.1 37.3 + - - +
91A ILE* 4.8 6.1 - - + -
117A ALA 3.6 1.0 + - - -
118A LYS* 1.3 72.6 - - - +
120A SER* 1.3 61.3 + - - +
121A CYS* 4.4 3.1 - - + -
219A PRO* 3.7 22.7 - - + -
231A TRP* 3.8 43.2 - + + -
234A LYS* 3.8 34.2 - - + -
237A MET* 4.5 4.3 - - + -
238A VAL* 3.7 31.4 - - + -
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Residues in contact with SER 120 (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* 3.4 5.0 - - - +
64A SER* 2.8 64.0 + - - -
66A SER* 4.1 11.0 + - - -
89A GLN* 5.8 4.0 - - - +
118A LYS* 3.9 5.3 + - - -
119A PHE* 1.3 76.6 - - - +
121A CYS* 1.3 60.6 + - - +
122A SER* 4.0 0.5 + - - -
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Residues in contact with CYS 121 (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* 2.0 50.7 - - - -
62A GLU 3.4 3.6 - - - -
119A PHE* 4.3 3.6 - - + -
120A SER* 1.3 72.8 - - - +
122A SER* 1.3 58.0 + - - +
123A GLY 3.4 20.9 - - - -
124A LYS* 4.3 6.6 - - + +
231A TRP* 3.7 33.0 - - + +
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Residues in contact with SER 122 (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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62A GLU* 2.7 41.9 + - - +
63A ALA* 4.4 2.6 + - - -
64A SER* 5.7 4.2 - - - -
120A SER 4.0 1.9 + - - -
121A CYS* 1.3 73.7 - - - +
123A GLY* 1.3 59.4 + - - +
124A LYS* 4.2 4.8 + - - +
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Residues in contact with GLY 123 (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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61A ILE* 3.0 35.7 + - - -
62A GLU* 3.1 21.8 + - - +
121A CYS* 3.4 6.7 - - - -
122A SER* 1.3 82.4 + - - +
124A LYS* 1.3 60.1 + - - -
125A ILE* 5.5 0.2 - - - -
202A LYS* 5.5 10.5 - - - -
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Residues in contact with LYS 124 (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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58A THR* 4.3 17.0 - - + -
59A TYR 3.4 11.9 - - - +
61A ILE 4.6 0.2 - - - +
121A CYS* 4.3 7.2 - - + +
122A SER 4.1 4.4 + - - +
123A GLY* 1.3 73.7 - - - +
125A ILE* 1.3 71.9 + - - +
126A THR* 4.3 0.7 + - - +
200A LYS 5.1 0.3 - - - +
202A LYS 5.4 2.3 + - - -
224A ALA 5.7 0.4 + - - -
225A ASP 4.6 4.6 + - - -
226A THR* 3.5 38.2 + - - +
231A TRP* 4.2 22.5 - - + -
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Residues in contact with ILE 125 (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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57A ARG 4.3 0.3 - - - +
58A THR* 3.4 4.8 - - - -
59A TYR* 2.8 45.5 + - + +
61A ILE* 3.7 35.2 - - + -
124A LYS* 1.3 84.0 - - - +
126A THR* 1.3 58.9 + - - +
199A MET* 3.8 35.2 - - + -
200A LYS 3.4 16.4 - - - +
201A MET* 3.7 44.4 - - + -
202A LYS* 4.5 6.5 - - + +
213A PHE* 4.7 5.9 - - + -
260A MET* 5.0 5.6 - - + -
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Residues in contact with THR 126 (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* 3.4 29.3 - - + +
57A ARG 4.0 3.4 - - - -
58A THR* 4.0 12.5 + - - -
124A LYS 4.3 0.8 + - - +
125A ILE* 1.3 74.3 - - - +
127A GLY* 1.3 58.5 + - - +
128A ASN* 3.6 12.2 + - - +
199A MET* 3.5 4.5 - - - +
200A LYS* 2.8 61.3 + - + +
213A PHE* 4.3 2.7 - - - -
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Residues in contact with GLY 127 (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 0.5 - - - +
56A LEU* 3.2 25.8 + - - +
57A ARG 3.1 16.5 + - - -
126A THR* 1.3 77.0 + - - +
128A ASN* 1.3 62.3 + - - -
197A ILE* 4.1 10.3 - - - -
198A LEU 3.7 5.2 - - - -
199A MET* 4.1 1.1 - - - -
213A PHE* 3.6 22.5 - - - -
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Residues in contact with ASN 128 (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* 3.6 42.6 + - + +
54A ALA 3.4 5.6 - - - +
55A LEU* 3.6 26.0 - - - +
126A THR* 3.6 21.9 + - - +
127A GLY* 1.3 73.3 - - - -
129A LEU* 1.3 60.7 + - - +
197A ILE* 3.7 5.0 - - - -
198A LEU* 2.8 49.7 + - + +
200A LYS* 5.4 2.6 - - - +
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Residues in contact with LEU 129 (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* 3.4 21.5 - - - +
54A ALA* 2.7 38.8 + - + +
55A LEU 4.9 1.3 - - - +
56A LEU* 3.8 30.0 - - + +
127A GLY 4.3 0.2 + - - -
128A ASN* 1.3 69.4 - - - +
130A VAL* 1.3 61.7 + - - +
131A GLN* 5.6 8.7 - - + +
193A PHE 6.2 0.2 - - - +
196A MET 5.4 1.6 - - - +
197A ILE* 3.8 23.3 - - + -
210A LYS* 4.2 22.0 - - - +
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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
------------------------------------------------------------
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