Contacts of the strand formed by residues 68 - 77 (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 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A THR* 4.8 1.0 - - - +
28A ILE* 3.4 23.0 - - + +
29A GLY* 4.1 24.5 - - - -
60A ARG* 3.3 31.2 - - - +
61A THR 3.4 8.1 - - - -
66A ASN 4.1 1.2 + - - -
67A GLU* 1.3 74.1 - - - +
69A VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 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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24A THR* 4.0 11.4 - - + +
28A ILE* 3.5 9.2 - - - -
60A ARG* 3.4 5.0 - - - +
61A THR* 2.7 54.4 + - + +
62A THR 4.1 0.9 - - - -
63A ASN* 3.6 47.8 - - + +
67A GLU* 3.9 2.7 - - + +
68A ALA* 1.3 77.3 - - - +
70A ALA* 1.3 62.8 + - - +
145A PHE* 5.9 0.4 - - + -
154A GLU* 5.4 2.5 - - - +
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Residues in contact with ALA 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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23A THR 4.1 8.3 - - - +
24A THR* 3.0 17.5 + - - +
25A PRO* 4.2 3.4 - - + -
28A ILE* 3.8 6.0 - - + +
37A ILE* 3.8 19.1 - - + -
58A GLN* 4.3 7.6 - - + -
59A TYR 3.1 11.0 - - - +
61A THR* 4.4 1.1 - - - -
69A VAL* 1.3 83.6 - - - +
71A ASP* 1.3 64.7 + - - +
144A GLY* 5.6 0.3 - - - -
145A PHE* 3.4 30.2 + - + +
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Residues in contact with ASP 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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58A GLN* 3.3 6.2 - - - +
59A TYR* 2.9 43.2 + - + -
61A THR* 3.8 18.4 - - + -
69A VAL* 5.7 0.4 - - + -
70A ALA* 1.3 75.1 - - - +
72A VAL* 1.3 76.9 + - - +
141A ASP* 2.6 37.4 - - - +
144A GLY* 3.6 19.1 - - - -
145A PHE* 3.6 14.4 - - - -
158A ALA* 3.4 18.7 - - - +
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Residues in contact with VAL 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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21A PHE* 3.7 39.9 - - + +
22A TYR* 4.1 10.3 - - + +
56A GLN* 4.1 16.4 - - + +
57A LEU 3.2 5.2 - - - +
58A GLN* 4.4 1.3 - - - -
59A TYR* 3.6 4.7 - - - -
71A ASP* 1.3 84.7 + - - +
73A ALA* 1.3 71.7 + - - +
104A SER* 3.8 27.6 - - - +
141A ASP* 3.0 37.0 + - - +
145A PHE* 4.0 9.2 - - + -
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Residues in contact with ALA 73 (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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56A GLN* 3.2 5.0 - - - -
57A LEU* 2.8 37.2 + - + +
59A TYR* 3.6 20.0 - - + -
72A VAL* 1.3 77.8 - - - +
74A THR* 1.3 61.8 + - - +
75A VAL* 4.4 2.4 + - + -
104A SER* 5.2 0.2 - - - -
138A VAL* 4.2 13.0 - - + -
139A SER 3.7 6.3 - - - +
140A SER* 3.7 19.5 - - - +
141A ASP* 4.4 1.1 - - - +
162A GLY* 4.5 4.7 - - - +
165A ALA* 5.8 0.2 - - + -
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Residues in contact with THR 74 (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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42A VAL* 4.9 4.3 - - + -
44A THR* 4.5 12.6 - - + -
54A SER* 4.8 2.0 - - - -
55A PHE 3.4 10.8 - - - +
56A GLN* 4.1 3.8 - - - +
73A ALA* 1.3 71.6 + - - +
75A VAL* 1.3 67.8 + - - +
76A TRP* 3.6 34.2 - - + -
104A SER* 3.4 32.3 + - - +
107A TYR* 3.8 11.2 - - + -
137A VAL 3.9 0.2 - - - +
138A VAL* 3.4 3.8 - - - +
139A SER 2.9 37.0 + - - -
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Residues in contact with VAL 75 (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 ALA 3.8 0.5 - - - +
54A SER* 3.1 8.1 - - - -
55A PHE* 2.9 59.7 + - + +
57A LEU* 3.9 31.9 - - + -
73A ALA* 5.0 0.9 - - + -
74A THR* 1.3 81.3 - - - +
76A TRP* 1.3 63.0 - - - +
77A ILE* 4.5 4.3 - - + -
137A VAL 3.1 8.5 - - - +
138A VAL* 3.9 19.3 - - + -
166A LEU* 3.9 22.9 - - + -
169A TYR* 4.4 10.1 - - + -
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Residues in contact with TRP 76 (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 THR* 2.9 23.2 + - - -
46A ILE* 3.8 19.6 - - + +
47A GLY* 3.5 24.2 - - - +
52A ALA* 4.1 4.0 - - + -
53A ALA 3.3 4.3 - - - +
54A SER* 3.5 14.5 - - - -
74A THR* 3.6 35.4 - - + -
75A VAL* 1.3 76.2 - - - +
77A ILE* 1.3 67.3 + - - +
78A PRO* 3.6 5.2 - - - +
107A TYR* 3.7 40.8 - + + -
127A ILE* 4.0 17.9 - - + -
131A LEU* 3.8 25.2 - - + +
136A TYR* 3.8 1.9 - - - +
137A VAL* 2.9 50.0 + - + +
139A SER* 4.1 8.7 - - - -
166A LEU* 5.5 0.2 - - - +
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Residues in contact with ILE 77 (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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52A ALA* 3.2 21.7 - - - +
53A ALA* 2.9 24.6 + - + +
55A PHE* 4.0 20.2 - - + -
75A VAL* 4.5 10.3 - - + -
76A TRP* 1.3 79.6 - - - +
78A PRO* 1.3 77.8 - - - +
81A PRO* 5.4 2.5 - - + -
136A TYR* 4.0 23.8 - - + +
166A LEU* 4.4 8.5 - - + -
170A GLN* 3.6 40.8 - - + +
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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