Contacts of the helix formed by residues 102 - 108 (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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PRO* 5.2 0.4 - - + -
22A TYR* 4.5 8.7 - - + -
94A GLU* 3.5 6.0 + - - +
99A LEU* 3.0 19.8 + - + +
100A ASP* 3.2 2.2 - - - -
101A CYS* 1.3 75.9 - - - +
103A PRO* 1.3 73.5 - - + +
104A SER* 3.9 6.3 - - - +
105A TYR* 3.4 9.1 + - + +
106A SER* 2.9 22.0 + - - -
141A ASP* 3.6 23.8 - - + +
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Residues in contact with PRO 103 (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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92A VAL* 4.1 31.4 - - + -
94A GLU* 3.3 22.0 - - + +
101A CYS 4.0 1.1 - - - +
102A ALA* 1.3 82.7 - - + +
104A SER* 1.3 63.3 + - - +
106A SER* 3.1 8.4 + - - +
107A TYR* 2.9 46.2 + - + -
118A THR* 5.7 0.7 - - - +
139A SER* 4.7 0.7 - - - +
140A SER 4.1 15.7 - - - +
141A ASP* 3.6 21.8 - - + +
142A HIS* 4.4 7.6 - - + -
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Residues in contact with SER 104 (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* 2.5 28.0 + - - -
56A GLN* 3.6 21.9 + - - -
72A VAL* 3.8 11.7 - - - -
73A ALA 5.2 0.2 - - - -
74A THR* 3.4 24.1 + - - +
102A ALA* 3.9 1.7 - - - +
103A PRO* 1.3 71.9 - - - +
105A TYR* 1.3 60.0 + - - +
107A TYR* 3.5 12.4 + - - +
108A LEU* 3.6 8.3 - - - +
139A SER 5.7 0.2 + - - -
141A ASP* 2.6 35.2 + - - -
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Residues in contact with TYR 105 (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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11A ALA* 3.7 30.4 + - + +
13A LEU* 3.8 4.6 + - + -
14A PRO 3.6 17.5 - - - -
15A ASN* 3.9 25.1 + - - +
16A PRO* 3.5 33.7 - - + -
22A TYR* 3.8 3.8 + - - +
100A ASP 3.3 20.6 - - - +
102A ALA* 3.4 9.6 + - + +
103A PRO 3.3 0.6 - - - -
104A SER* 1.3 78.8 + - - +
106A SER* 1.3 57.8 + - - +
108A LEU* 3.5 21.4 - - + +
112A ASP* 4.5 7.1 + - - -
113A GLN* 2.9 53.8 + - + +
114A PRO* 4.0 13.0 - - + -
224B PHE* 5.5 2.1 - - - -
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Residues in contact with SER 106 (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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100A ASP 4.9 1.4 + - - -
101A CYS 3.8 1.9 + - - -
102A ALA 2.9 14.3 + - - -
103A PRO* 3.1 11.3 + - - -
105A TYR* 1.3 76.1 - - - +
107A TYR* 1.3 59.5 + - - +
108A LEU 3.7 0.2 + - - -
113A GLN* 3.7 10.7 + - - +
115A ASN* 3.4 40.6 + - - +
116A LYS* 3.5 26.0 + - - +
118A THR* 4.3 4.3 + - - -
119A ALA* 3.5 18.7 - - - +
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Residues in contact with TYR 107 (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* 3.2 31.2 - - + -
45A ASP* 3.3 9.9 + - - +
46A ILE* 4.0 9.6 + - + +
74A THR* 3.8 17.7 - - + -
76A TRP* 3.7 25.1 - + + -
90A TYR* 3.6 8.8 - - - -
92A VAL* 2.9 20.6 - - + +
103A PRO* 2.9 38.6 + - + +
104A SER 3.6 5.6 - - - +
105A TYR 3.3 0.4 - - - -
106A SER* 1.3 74.7 - - - +
108A LEU* 1.3 65.3 + - - +
119A ALA* 3.9 15.3 - - + -
123A THR* 3.8 14.1 - - + -
127A ILE* 3.7 10.9 - - + +
139A SER* 2.6 41.8 + - - -
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Residues in contact with LEU 108 (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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11A ALA* 4.4 1.8 - - + -
12A ALA* 4.5 2.2 - - + -
13A LEU* 3.9 37.5 - - + +
42A VAL* 3.8 21.8 - - + -
43A PRO* 3.3 18.2 - - + +
44A THR* 4.1 1.6 - - + +
45A ASP* 3.6 8.2 - - - +
56A GLN* 3.7 21.1 - - - +
104A SER 3.6 6.7 - - - +
105A TYR* 3.5 39.7 - - + +
106A SER 3.4 0.6 - - - -
107A TYR* 1.3 80.5 - - - +
109A THR* 1.3 69.3 + - - +
110A GLY 3.4 0.9 + - - -
113A GLN* 2.9 19.6 + - - +
116A LYS* 3.8 2.1 - - - -
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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