Contacts of the strand formed by residues 39 - 56 (chain A) in PDB entry 2Q53
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 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER 3.5 4.7 + - - +
38A ALA* 1.3 72.9 - - - +
40A PHE* 1.3 68.0 + - - +
41A PHE 3.2 0.2 + - - -
84A TRP* 3.3 5.7 - - - -
85A LYS* 2.7 50.1 + - + +
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Residues in contact with PHE 40 (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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39A ALA* 1.3 75.6 - - - +
41A PHE* 1.3 64.3 + - - +
42A CYS* 3.6 29.4 - - - -
43A VAL* 3.9 18.2 - - + -
82A VAL* 3.5 29.8 - - + -
84A TRP* 3.2 24.3 - + + -
85A LYS* 5.5 0.2 - - - +
150A ASN* 3.8 28.3 - - + +
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Residues in contact with PHE 41 (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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18A LEU* 4.0 23.3 - - + -
40A PHE* 1.3 84.5 - - - +
42A CYS* 1.3 71.3 + - + +
83A VAL* 2.7 43.5 + - + +
85A LYS* 4.0 40.8 - - + +
118A LYS* 5.7 8.5 - - - -
120A ILE* 4.3 16.4 - - + -
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Residues in contact with CYS 42 (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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40A PHE* 3.6 17.9 - - - -
41A PHE* 1.3 90.2 - - + +
43A VAL* 1.3 63.3 + - - +
44A ALA* 4.7 0.4 - - - -
82A VAL* 3.3 2.6 - - - +
83A VAL* 2.5 51.4 + - - +
114A THR* 3.8 15.3 - - + -
120A ILE* 3.3 34.1 - - - -
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Residues in contact with VAL 43 (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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40A PHE* 3.9 17.4 - - + -
42A CYS* 1.3 74.8 - - - +
44A ALA* 1.3 64.6 + - - +
80A TRP* 3.9 22.7 - - + -
81A GLY 3.5 12.3 - - - +
82A VAL* 4.1 1.8 - - + -
114A THR* 3.3 25.3 - - - +
115A GLN* 4.4 12.5 + - + +
150A ASN 3.2 26.9 - - - +
151A GLY 4.4 3.6 - - - +
152A LEU* 4.0 26.2 - - + -
153A PRO* 4.4 1.6 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.8 5.3 - - + -
42A CYS* 4.0 2.6 + - - -
43A VAL* 1.3 79.1 - - - +
45A ARG* 1.3 60.7 + - - +
80A TRP* 3.2 12.7 - - - -
81A GLY 3.0 30.5 + - - -
82A VAL* 4.8 0.2 - - - +
83A VAL* 4.1 12.8 - - + -
112A VAL* 3.5 29.8 - - + -
113A ALA* 3.5 16.8 - - - +
114A THR 4.0 0.9 - - - +
120A ILE* 5.3 0.4 - - + -
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Residues in contact with ARG 45 (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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44A ALA* 1.3 74.7 - - - +
46A LEU* 1.3 63.3 + - - +
47A GLN* 3.5 31.5 + - - +
78A GLU* 3.4 36.6 + - + -
79A VAL 3.5 5.6 - - - +
80A TRP* 3.4 43.1 - - + +
112A VAL* 3.3 19.3 - - - +
113A ALA* 3.0 19.2 + - - +
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Residues in contact with LEU 46 (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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20A PHE* 4.0 18.4 - - + -
45A ARG* 1.3 73.8 - - - +
47A GLN* 1.3 66.3 + - - +
49A PHE* 3.3 50.2 - - + +
71A ILE* 3.6 22.7 - - + -
78A GLU* 3.3 1.6 - - - -
79A VAL* 2.6 43.1 + - + +
110A VAL* 4.4 15.5 - - + -
111A LYS 4.2 11.9 - - - +
112A VAL* 3.9 17.9 - - + -
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Residues in contact with GLN 47 (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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45A ARG* 3.5 42.0 + - - +
46A LEU* 1.3 75.5 - - - +
48A ASP* 1.3 93.3 + - - +
49A PHE* 3.1 17.8 + - - -
76A GLY* 3.3 21.2 + - - -
77A ASP 2.9 21.7 + - - -
78A GLU* 3.7 11.3 - - - +
111A LYS 5.7 0.4 + - - -
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Residues in contact with ASP 48 (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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47A GLN* 1.3 96.9 + - - +
49A PHE* 1.3 54.7 + - + +
73A GLN* 3.1 11.5 - - + +
74A SER 2.6 40.7 + - - +
75A PRO* 3.8 21.3 - - - +
76A GLY 4.0 2.6 + - - -
77A ASP 2.9 10.8 + - - -
101B LYS 4.4 12.4 - - - +
102B SER* 4.3 14.2 - - - +
103B GLY* 5.9 3.6 - - - -
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Residues in contact with PHE 49 (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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46A LEU* 3.3 50.0 - - + +
47A GLN 3.1 9.3 - - - -
48A ASP* 1.3 81.6 - - + +
50A LYS* 1.3 58.9 + - - +
71A ILE* 3.9 11.0 - - + -
72A PHE* 3.2 24.5 - - - -
73A GLN* 3.4 28.5 - - + -
77A ASP* 3.7 3.3 + - - -
78A GLU* 3.2 21.5 + - - -
79A VAL* 3.2 15.9 - - + +
110A VAL* 5.3 5.6 - - + -
126A LEU* 4.0 21.1 - - + -
106B VAL* 3.4 30.3 - - + -
128B THR* 4.6 0.7 - - - -
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Residues in contact with LYS 50 (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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49A PHE* 1.3 73.8 - - - +
51A LEU* 1.3 75.3 + - - +
52A ASP* 5.9 0.4 - - - -
71A ILE* 3.3 6.2 - - - +
72A PHE* 2.8 57.5 + - + -
74A SER* 3.7 12.1 - - - +
77A ASP* 3.1 35.9 + - - +
78A GLU 5.0 1.1 - - - +
79A VAL* 3.8 2.9 - - - -
159A LYS* 5.4 6.5 - - - +
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Residues in contact with LEU 51 (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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22A TYR* 3.7 38.1 - - + +
50A LYS* 1.3 96.2 + - - +
52A ASP* 1.3 80.5 + - - +
53A PHE* 3.9 22.9 - - + -
69A ALA* 4.4 8.3 - - + -
70A THR 3.8 8.1 - - - +
71A ILE* 4.0 3.6 - - + -
78A GLU 5.1 1.9 + - - +
79A VAL* 3.7 7.4 - - + +
143A ILE* 5.9 0.7 - - + -
156A TYR* 3.9 19.3 - - + +
160A LEU* 3.8 28.9 - - + -
163A ILE* 4.5 3.6 - - + -
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Residues in contact with ASP 52 (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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50A LYS* 5.9 0.7 - - - -
51A LEU* 1.3 83.0 - - - +
53A PHE* 1.3 96.5 + - - +
69A ALA* 3.5 1.7 - - - -
70A THR* 3.0 31.1 + - + +
72A PHE* 4.1 14.5 - - + -
130A TYR* 2.6 33.3 + - - +
132A SER* 3.1 22.9 + - - -
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Residues in contact with PHE 53 (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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51A LEU* 3.9 24.9 - - + -
52A ASP* 1.3 90.4 + - - +
54A GLY* 1.3 59.2 + - - +
67A GLY 4.0 4.7 - - - -
68A ILE 3.3 6.5 - - - +
69A ALA* 3.7 13.5 - - + -
70A THR* 4.7 0.7 - - - +
130A TYR* 4.0 2.9 - - - -
132A SER* 3.3 8.5 - - - -
133A ALA 2.9 31.8 + - - +
134A PRO* 4.8 0.2 - - + -
135A PRO* 3.8 26.2 - - + -
139A TYR* 3.5 35.2 - + - -
140A LYS* 6.2 1.1 - - - -
143A ILE* 3.8 17.9 - - + -
163A ILE* 3.7 37.0 - - + -
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Residues in contact with GLY 54 (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 PHE* 1.3 77.5 - - - +
55A ASN* 1.3 61.0 + - - +
56A SER 3.9 0.2 - - - -
67A GLY* 3.4 7.3 - - - -
68A ILE* 2.9 41.1 + - - +
127A MSE 4.1 5.3 - - - +
130A TYR* 3.8 8.5 - - - -
131A GLU 3.3 12.3 - - - -
133A ALA 3.5 8.5 + - - -
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Residues in contact with ASN 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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54A GLY* 1.3 75.3 - - - +
56A SER* 1.3 66.2 + - - +
57A GLN 3.3 1.0 + - - -
58A GLY* 3.0 20.2 + - - -
59A LYS 2.9 22.6 - - - +
60A THR* 3.3 31.3 + - - +
61A SER 4.4 0.7 + - - -
66A GLY 4.3 2.3 - - - +
67A GLY* 4.2 7.4 + - - -
68A ILE* 5.4 0.2 - - - -
130A TYR* 3.6 2.8 - - - +
131A GLU* 3.0 30.1 + - + +
133A ALA* 3.2 25.3 - - - +
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Residues in contact with SER 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 GLY 3.8 3.6 + - - -
55A ASN* 1.3 64.1 - - - +
57A GLN* 1.3 66.2 + - - +
58A GLY 2.9 1.6 - - - -
59A LYS* 2.6 37.8 + - - +
68A ILE* 4.6 6.6 - - - +
103A GLY 4.2 0.9 + - - -
104A MSE 3.2 48.9 + - - +
127A MSE 3.5 28.0 - - - -
129A ASN 3.9 5.9 + - - -
130A TYR* 4.2 0.2 - - - -
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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