Contacts of the helix formed by residues 102 - 108 (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 102 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PRO* 5.1 0.4 - - + -
22B TYR* 4.5 9.4 - - + -
94B GLU* 3.5 6.1 + - - +
99B LEU* 3.0 18.6 + - + +
100B ASP 3.2 1.6 - - - -
101B CYS* 1.3 75.7 - - - +
103B PRO* 1.4 73.5 - - + +
104B SER* 3.3 5.8 + - - +
105B TYR* 3.4 9.3 + - + +
106B SER* 3.0 21.5 + - - -
141B ASP* 3.6 24.0 - - + +
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Residues in contact with PRO 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 4.0 32.3 - - + -
94B GLU* 3.4 19.3 - - + +
101B CYS 3.6 1.5 - - - +
102B ALA* 1.4 82.3 - - + +
104B SER* 1.3 56.7 + - - +
106B SER* 3.0 9.9 + - - +
107B TYR* 2.9 50.8 + - + -
118B THR* 5.6 0.4 - - - +
119B ALA* 6.4 0.2 - - + -
139B SER* 4.5 1.6 - - - +
140B SER 3.8 18.4 - - - +
141B ASP* 3.3 21.8 - - + +
142B HIS* 4.5 6.7 - - + -
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 2.7 24.5 + - - -
56B GLN* 3.6 14.0 + - - -
72B VAL* 3.8 11.4 - - - -
73B ALA 5.1 0.7 - - - -
74B THR* 3.3 24.9 + - - +
102B ALA* 3.9 1.2 - - - +
103B PRO* 1.3 72.1 - - - +
105B TYR* 1.3 62.0 + - - +
107B TYR* 3.5 9.8 + - - +
108B LEU* 3.6 15.1 + - - +
141B ASP* 2.5 38.5 + - - -
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Residues in contact with TYR 105 (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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11B ALA* 3.9 18.3 + - + +
13B LEU 3.9 10.6 + - - -
14B PRO 3.5 18.4 - - - -
15B ASN* 3.8 21.4 + - - +
16B PRO* 3.5 38.4 - - + -
22B TYR* 3.6 5.3 + + - +
100B ASP 3.4 20.9 - - - +
102B ALA* 3.4 9.8 + - + +
103B PRO 3.4 0.4 - - - -
104B SER* 1.3 80.1 + - - +
106B SER* 1.3 59.3 + - - +
108B LEU* 3.2 24.5 + - + +
112B ASP* 4.6 9.9 + - - -
113B GLN* 3.0 46.9 + - + +
114B PRO* 3.8 17.2 - - + +
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Residues in contact with SER 106 (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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100B ASP 5.0 1.2 + - - -
101B CYS 3.7 9.7 + - - -
102B ALA 3.0 14.3 + - - -
103B PRO* 3.0 10.6 + - - -
105B TYR* 1.3 78.5 - - - +
107B TYR* 1.3 59.3 + - - +
108B LEU 3.5 0.3 + - - -
113B GLN* 3.7 12.5 + - - +
115B ASN* 3.4 34.1 + - - +
116B LYS* 3.6 21.3 + - - +
118B THR* 4.2 5.1 + - - -
119B ALA* 3.4 21.1 - - - +
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Residues in contact with TYR 107 (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* 3.4 31.9 - - + -
45B ASP* 3.4 9.2 + - - +
46B ILE* 3.9 18.6 + - + +
74B THR* 3.9 16.2 - - + -
76B TRP* 3.8 22.7 - + + -
90B TYR* 3.5 10.0 - - - -
92B VAL* 2.9 18.9 - - + +
103B PRO* 2.9 36.7 + - + +
104B SER 3.7 5.6 - - - +
105B TYR 3.3 0.2 - - - -
106B SER* 1.3 71.9 - - - +
108B LEU* 1.3 67.5 + - - +
119B ALA* 3.9 13.7 - - + -
123B THR* 3.6 24.0 - - + -
127B ILE* 4.9 1.5 - - + +
139B SER* 2.8 38.2 + - - -
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Residues in contact with LEU 108 (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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11B ALA* 4.6 0.7 - - + -
12B ALA* 4.4 3.1 - - + +
13B LEU* 3.6 42.0 - - + +
22B TYR* 5.9 0.4 - - - +
42B VAL* 3.7 34.5 - - + -
43B PRO* 3.5 12.8 - - + +
44B THR* 4.6 1.3 - - + -
45B ASP* 3.9 0.4 - - - -
56B GLN* 3.8 13.2 - - - +
104B SER 3.6 7.2 - - - +
105B TYR* 3.2 36.8 + - + +
107B TYR* 1.3 77.0 - - - +
109B THR* 1.3 68.3 + - - +
113B GLN* 3.0 10.6 + - - +
116B LYS* 2.9 24.6 + - - -
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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