Contacts of the strand formed by residues 53 - 62 (chain A) in PDB entry 3GUU
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LYS* 3.8 21.1 - - - +
51A ASN 4.3 0.8 + - - -
52A ALA* 1.3 69.2 - - - +
54A SER* 1.3 60.0 + - - +
55A PHE* 3.8 21.3 - - + -
76A TRP* 3.3 2.6 - - - -
77A ILE* 2.9 41.6 + - + +
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Residues in contact with SER 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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41A LYS* 3.7 8.5 - - - +
42A VAL* 2.8 51.4 + - - +
44A THR* 2.8 35.5 + - - +
47A GLY* 4.4 1.0 - - - -
52A ALA 3.5 2.8 + - - -
53A ALA* 1.3 73.4 - - - +
55A PHE* 1.3 62.6 + - - +
74A THR* 4.8 1.3 - - - -
75A VAL 3.1 10.8 - - - -
76A TRP* 3.5 14.3 - - - -
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Residues in contact with PHE 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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39A SER* 5.8 0.2 - - - -
40A ARG 3.2 9.6 - - - +
41A LYS* 3.5 51.4 - - + -
42A VAL* 4.1 3.4 - - - +
53A ALA* 3.8 23.1 - - + -
54A SER* 1.3 76.1 - - - +
56A GLN* 1.3 61.9 + - - +
57A LEU* 4.4 6.7 - - + -
73A ALA 4.0 0.2 - - - +
74A THR* 3.4 4.5 - - - +
75A VAL* 2.9 44.5 + - + +
77A ILE* 4.0 20.2 - - + -
169A TYR* 3.2 37.7 - + + +
170A GLN* 5.2 1.6 - - - -
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Residues in contact with GLN 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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13A LEU* 4.1 4.4 - - - +
21A PHE* 3.8 14.5 - - + -
22A TYR* 3.9 7.5 + - - -
39A SER* 3.3 4.5 - - - -
40A ARG* 2.8 68.7 + - + -
42A VAL* 4.0 16.7 - - + +
55A PHE* 1.3 73.7 - - - +
57A LEU* 1.3 63.0 + - - +
72A VAL* 4.1 5.1 - - + +
73A ALA 3.2 9.9 - - - +
74A THR* 4.1 10.1 - - - +
104A SER* 3.6 34.7 + - - -
108A LEU* 3.7 20.0 - - - +
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Residues in contact with LEU 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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21A PHE* 4.3 2.5 - - - -
36A VAL* 4.4 10.5 - - + -
38A GLN 3.8 3.1 - - - +
39A SER* 3.6 17.0 - - - -
55A PHE* 4.4 4.7 - - + -
56A GLN* 1.3 77.4 - - - +
58A GLN* 1.3 62.7 + - - +
59A TYR* 3.6 5.2 - - + -
72A VAL* 3.2 5.2 - - - +
73A ALA* 2.8 34.3 + - + +
75A VAL* 3.9 31.0 - - + -
162A GLY 5.3 0.4 - - - +
165A ALA* 3.8 26.0 - - + +
166A LEU* 4.0 1.6 - - - +
169A TYR* 3.5 55.4 - - + -
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Residues in contact with GLN 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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20A PRO 3.9 3.2 + - - -
21A PHE* 2.8 45.1 + - + +
23A THR 3.1 22.2 + - - -
25A PRO* 4.9 4.3 - - - +
36A VAL* 3.6 1.6 - - - -
37A ILE* 2.7 49.2 + - + +
38A GLN* 2.8 56.1 + - + +
57A LEU* 1.3 72.7 - - - +
59A TYR* 1.3 55.8 + - - +
70A ALA* 4.3 11.2 - - + +
71A ASP 3.3 10.3 - - - +
72A VAL* 4.4 1.6 - - + -
145A PHE* 4.9 0.2 - - + -
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Residues in contact with TYR 59 (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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34A GLY* 4.4 1.3 - - - -
35A GLN 3.3 14.6 - - - +
36A VAL* 4.3 1.8 - - + -
37A ILE* 3.8 7.0 - - - +
57A LEU 3.6 11.9 - - - -
58A GLN* 1.3 76.2 - - - +
60A ARG* 1.3 77.5 + - - +
61A THR* 3.9 11.0 - - + -
70A ALA* 3.1 4.0 - - - -
71A ASP* 2.9 55.8 + - + +
72A VAL 3.6 11.9 - - - -
73A ALA* 3.6 23.6 - - + -
140A SER* 3.4 13.3 + - - -
158A ALA 2.6 23.4 + - - -
161A ASP* 3.5 21.8 - - + -
162A GLY* 3.3 19.1 - - - -
165A ALA* 3.8 22.9 - - + -
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Residues in contact with ARG 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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28A ILE* 3.6 29.2 - - + +
29A GLY 4.9 3.4 + - - -
31A PHE* 3.0 38.7 + - + -
32A ALA* 3.5 19.6 - - - +
33A LYS* 3.7 29.9 - - - +
34A GLY* 2.9 25.6 + - - -
35A GLN 3.1 9.6 + - - +
37A ILE* 3.8 1.4 - - + +
59A TYR* 1.3 77.8 - - - +
61A THR* 1.3 78.7 + - - +
62A THR* 3.3 18.8 + - - +
66A ASN 5.7 0.4 + - - -
67A GLU 4.8 0.2 - - - -
68A ALA* 3.3 29.5 - - - +
69A VAL 3.4 10.1 - - - +
161A ASP* 3.8 0.2 - - - +
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Residues in contact with THR 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* 3.9 4.7 - - + -
60A ARG* 1.3 94.7 + - - +
62A THR* 1.3 68.9 + - - +
68A ALA* 3.4 0.5 - - - -
69A VAL* 2.7 38.3 + - + +
71A ASP* 3.8 29.4 - - + -
157A MET 3.4 16.3 + - - -
158A ALA* 3.5 13.6 + - + -
161A ASP* 2.7 30.3 + - - -
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Residues in contact with THR 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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33A LYS* 3.5 8.5 - - - +
60A ARG* 3.3 19.7 + - - +
61A THR* 1.3 83.6 + - - +
63A ASN* 1.3 76.3 + - - +
66A ASN* 3.6 27.4 - - + +
67A GLU 3.3 5.2 - - - +
69A VAL* 4.1 3.8 - - - -
153A TYR 4.9 0.7 - - - +
154A GLU* 4.7 5.0 - - - +
157A MET* 3.6 32.6 - - + +
200A TYR* 2.8 25.1 + - + -
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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