Contacts of the strand formed by residues 68 - 77 (chain B) 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 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 4.5 1.6 - - - +
28B ILE* 3.7 35.6 - - + +
29B GLY* 4.4 8.5 - - - -
60B ARG* 3.6 31.5 - - - +
61B THR 3.4 7.9 - - - -
66B ASN 4.2 0.8 + - - -
67B GLU* 1.3 73.4 - - - +
69B VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 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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24B THR* 4.0 11.2 - - + +
28B ILE* 3.6 9.0 - - - +
60B ARG* 3.5 3.6 - - - -
61B THR* 2.8 47.6 + - + +
62B THR 4.4 0.9 - - - -
63B ASN* 3.6 39.9 - - + +
67B GLU* 4.0 3.6 - - + +
68B ALA* 1.3 79.5 - - - +
70B ALA* 1.3 71.2 + - - +
71B ASP* 5.7 0.2 - - + -
145B PHE* 5.9 0.4 - - + +
154B GLU* 5.4 2.7 - - - +
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Residues in contact with ALA 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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23B THR 4.2 0.4 - - - +
24B THR* 3.0 18.6 + - - +
25B PRO* 4.1 10.3 - - + -
28B ILE* 3.8 4.0 - - + +
37B ILE* 3.8 20.6 - - + -
58B GLN* 4.2 10.1 - - + -
59B TYR 3.2 10.1 - - - +
61B THR* 4.5 0.2 - - - -
69B VAL* 1.3 86.3 - - - +
71B ASP* 1.3 64.0 + - - +
144B GLY* 5.6 0.2 - - - -
145B PHE* 3.4 31.3 + - + +
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Residues in contact with ASP 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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58B GLN* 3.3 6.4 - - - +
59B TYR* 2.9 45.5 + - + -
61B THR* 3.8 17.7 - - + -
70B ALA* 1.3 74.5 - - - +
72B VAL* 1.3 77.2 + - - +
141B ASP* 2.6 36.6 - - - +
144B GLY* 3.7 19.0 - - - -
145B PHE* 3.8 13.0 - - - -
158B ALA* 3.5 18.7 - - - +
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Residues in contact with VAL 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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21B PHE* 3.8 33.9 - - + +
22B TYR* 3.9 11.9 - - + -
56B GLN* 4.2 16.4 - - + +
57B LEU 3.4 6.5 - - - +
58B GLN* 4.6 1.3 - - - -
59B TYR* 3.6 4.5 - - - -
71B ASP* 1.3 84.8 + - - +
73B ALA* 1.3 69.5 + - - +
104B SER* 3.7 25.8 - - - +
141B ASP* 2.9 39.5 + - - +
145B PHE* 3.9 16.6 - - + -
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Residues in contact with ALA 73 (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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56B GLN* 3.3 7.1 - - - +
57B LEU* 2.9 37.4 + - + +
59B TYR* 3.5 19.7 - - + -
72B VAL* 1.3 76.9 - - - +
74B THR* 1.3 63.4 + - - +
75B VAL* 5.0 1.8 - - + -
104B SER* 5.1 0.4 - - - -
138B VAL* 3.9 14.4 - - + -
139B SER 3.6 6.5 - - - +
140B SER* 3.7 20.9 - - - +
141B ASP* 4.3 0.7 - - - +
162B GLY* 4.7 2.7 - - - +
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Residues in contact with THR 74 (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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42B VAL* 5.0 3.1 - - + -
44B THR* 4.4 13.5 - - + -
54B SER* 4.9 1.1 - - - -
55B PHE 3.4 11.4 - - - +
56B GLN* 4.2 4.4 - - - +
73B ALA* 1.3 72.8 + - - +
75B VAL* 1.3 66.2 + - - +
76B TRP* 3.4 39.9 - - + -
104B SER* 3.3 34.9 + - - +
107B TYR* 3.9 7.9 - - + -
138B VAL* 3.4 3.1 - - - +
139B SER 2.9 36.4 + - - -
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Residues in contact with VAL 75 (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 ALA 3.8 0.3 - - - +
54B SER* 3.2 7.1 - - - -
55B PHE* 2.8 54.6 + - + +
57B LEU* 3.8 26.5 - - + -
73B ALA* 5.0 0.4 - - + -
74B THR* 1.3 78.6 - - - +
76B TRP* 1.3 63.3 + - - +
77B ILE* 4.2 17.3 - - + -
137B VAL 3.1 8.7 - - - +
138B VAL* 3.9 19.3 - - + -
166B LEU* 4.0 23.6 - - + -
169B TYR* 4.5 9.2 - - + -
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Residues in contact with TRP 76 (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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44B THR* 3.1 20.7 + - + -
46B ILE* 3.8 18.0 - - + +
47B GLY* 3.5 23.2 - - - +
52B ALA* 4.2 4.3 - - + -
53B ALA 3.3 3.8 - - - +
54B SER* 3.5 16.3 - - - -
74B THR* 3.4 38.6 - - + -
75B VAL* 1.3 77.7 - - - +
77B ILE* 1.3 67.1 + - - +
78B PRO* 3.7 5.1 - - - +
107B TYR* 3.8 41.5 - + + -
127B ILE* 4.2 9.4 - - + -
131B LEU* 3.6 24.1 - - + +
136B TYR* 3.8 2.3 - - - +
137B VAL* 2.8 56.9 + - + +
139B SER* 4.3 10.1 - - - -
166B LEU* 5.6 0.2 - - - +
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Residues in contact with ILE 77 (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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52B ALA* 3.3 20.8 - - - +
53B ALA* 3.0 15.5 + - + +
55B PHE* 3.8 26.0 - - + -
75B VAL* 4.2 18.6 - - + -
76B TRP* 1.3 77.9 - - - +
78B PRO* 1.4 78.3 - - - +
79B ALA* 4.4 0.5 - - - -
81B PRO* 5.6 1.8 - - + -
136B TYR* 3.8 24.5 - - + +
166B LEU* 4.2 3.6 - - + -
169B TYR* 4.6 0.9 - - + -
170B GLN* 3.5 42.8 - - + +
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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