Contacts of the helix formed by residues 103 - 113 (chain B) in PDB entry 3Q41
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 THR 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B HIS* 4.5 3.4 - - + -
68B LYS 3.4 23.8 - - - +
69B PRO* 3.7 21.1 - - + +
71B ALA* 6.0 2.5 - - + +
74B MET* 3.8 14.4 - - - +
92B VAL* 4.6 2.2 - - - -
94B HIS* 3.1 27.7 - - - +
100B ASP* 2.8 37.5 + - - +
102B PHE* 1.3 71.0 - - - +
104B PRO* 1.4 59.2 - - - +
105B THR 3.5 0.2 - - - -
106B PRO* 3.4 19.4 - - + +
107B VAL* 3.8 10.2 - - - +
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Residues in contact with PRO 104 (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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92B VAL* 3.8 24.8 - - + +
94B HIS* 3.4 22.7 - - + +
101B HIS 4.0 0.2 - - - +
102B PHE* 3.2 3.8 - - - +
103B THR* 1.4 91.3 - - - +
105B THR* 1.3 62.4 + - - -
106B PRO 3.3 0.2 - - - -
107B VAL* 3.0 4.6 + - + +
108B SER* 2.8 23.6 + - - -
123B THR* 3.3 31.9 - - + -
128B TYR* 3.3 24.9 - - + +
137B PHE* 4.4 9.9 - - + -
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Residues in contact with THR 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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72A ILE* 6.1 3.6 - - + -
71B ALA* 5.7 0.5 - - - +
102B PHE* 2.5 36.2 + - + +
104B PRO* 1.3 73.0 - - - +
106B PRO* 1.4 67.8 - - - +
108B SER* 3.4 1.0 + - - -
109B TYR* 2.9 41.3 + - + -
127B ILE* 5.1 4.3 - - + -
128B TYR* 3.0 37.3 + - + +
134B HIS* 3.8 17.5 - - + +
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Residues in contact with PRO 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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109A TYR* 4.9 7.4 - - + +
71B ALA* 3.4 41.7 - - + +
74B MET* 3.7 13.0 - - + -
75B ALA* 3.7 15.9 - - + +
102B PHE 3.6 3.4 - - - +
103B THR* 3.4 20.4 - - - +
105B THR* 1.4 98.7 - - - +
107B VAL* 1.3 51.6 + - - +
109B TYR* 3.3 6.4 + - + +
110B THR* 2.8 40.8 + - - -
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Residues in contact with VAL 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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32B VAL* 4.0 11.2 - - + -
74B MET* 3.8 22.9 - - + -
78B VAL* 3.8 28.2 - - + +
90B ILE* 4.2 19.1 - - + -
92B VAL* 3.6 26.9 - - + -
103B THR 3.8 17.3 - - - +
104B PRO 3.0 5.8 + - - +
106B PRO* 1.3 74.5 - - - +
108B SER* 1.3 57.8 + - - +
110B THR* 4.1 0.8 - - - -
111B ALA* 2.9 35.5 + - - +
118B VAL* 4.3 7.6 - - + -
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Residues in contact with SER 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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104B PRO 2.8 19.3 + - - -
105B THR* 3.7 2.7 - - - -
107B VAL* 1.3 72.9 - - - +
109B TYR* 1.3 52.6 + - - +
111B ALA* 4.3 0.2 - - - +
112B GLY* 2.7 35.9 + - - -
118B VAL* 4.2 13.3 - - - +
128B TYR* 4.8 0.7 - - - -
134B HIS* 2.8 35.3 + - - +
136B SER* 5.0 4.4 + - - -
137B PHE* 3.8 30.2 + - - +
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Residues in contact with TYR 109 (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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71A ALA 5.0 1.0 + - - -
72A ILE* 6.0 0.3 - - - -
75A ALA* 3.4 25.2 - - + +
106A PRO* 5.0 8.0 - - + +
109A TYR* 3.5 60.9 - + + +
110A THR* 4.0 17.9 - - - -
113A PHE* 5.4 6.6 - + + -
105B THR* 2.9 37.2 + - + +
106B PRO 3.8 2.0 - - - +
108B SER* 1.3 76.2 - - - +
110B THR* 1.3 63.1 + - - +
112B GLY* 4.0 0.8 - - - -
113B PHE* 3.2 21.1 + - - +
133B ILE* 4.1 22.4 - - + +
134B HIS* 3.8 29.9 + + - -
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Residues in contact with THR 110 (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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109A TYR* 4.1 6.7 + - - -
132A SER 5.3 0.2 - - - +
133A ILE* 3.4 25.9 - - + +
75B ALA* 3.4 18.2 - - - +
78B VAL* 4.0 16.2 - - + -
79B CYS* 3.7 30.3 - - - -
83B ILE* 4.3 2.2 - - + -
106B PRO 2.8 26.9 + - - -
107B VAL 4.1 2.0 - - - -
109B TYR* 1.3 72.5 - - - +
111B ALA* 1.3 59.5 + - - +
113B PHE* 3.1 24.1 - - - +
114B TYR* 3.8 9.3 - - + -
308B CYS* 4.6 0.4 - - - -
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Residues in contact with ALA 111 (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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78B VAL* 4.7 0.7 - - + -
83B ILE* 4.0 11.9 - - + -
90B ILE* 4.1 17.7 - - + -
107B VAL 2.9 17.3 + - - +
110B THR* 1.3 74.2 - - - +
112B GLY* 1.3 63.7 + - - +
113B PHE 3.1 2.2 - - - -
114B TYR* 3.2 4.5 + - - +
115B ARG 3.2 3.6 + - - -
116B ILE* 3.0 40.6 + - + +
118B VAL* 3.5 22.0 - - + -
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Residues in contact with GLY 112 (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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113A PHE* 2.9 30.2 - - - -
108B SER 2.7 24.9 + - - -
109B TYR* 4.0 0.9 - - - -
110B THR 3.3 0.2 - - - -
111B ALA* 1.3 71.2 - - - +
113B PHE* 1.3 63.4 + - - +
114B TYR 3.2 0.2 - - - -
115B ARG* 3.0 13.6 + - - -
116B ILE 4.4 0.4 + - - -
136B SER* 3.6 24.2 - - - -
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Residues in contact with PHE 113 (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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108A SER 5.7 0.2 - - - -
109A TYR* 5.3 6.3 - + - -
112A GLY* 3.1 39.3 - - - -
113A PHE* 4.4 4.7 - - - +
115A ARG* 2.8 58.6 + - - +
132A SER 6.1 0.4 - - - -
133A ILE 5.7 4.9 - - - -
135A LEU* 3.9 34.1 - - + -
136A SER* 5.0 2.7 - - - -
109B TYR 3.2 12.7 + - - +
110B THR* 3.1 19.3 - - - +
112B GLY* 1.3 75.8 - - - +
114B TYR* 1.3 89.7 + + + +
115B ARG* 3.3 9.9 + - - +
311B ASN 4.2 6.3 - - - -
312B THR* 4.4 1.8 - - + -
314B ILE* 3.5 0.5 - - - +
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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