Contacts of the helix formed by residues 109 - 124 (chain B) in PDB entry 3X0X
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 SER 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B ILE 4.8 0.2 - - - +
105B GLU* 5.8 0.2 - - - -
108B GLY* 1.3 76.2 - - - -
110B GLN* 1.3 58.4 + - - +
111B GLU* 3.2 10.3 + - - +
112B GLN* 3.0 39.6 + - - +
113B GLU* 2.9 30.1 + - - +
232B GLY 5.1 0.6 - - - +
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Residues in contact with GLN 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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66B TYR* 4.7 5.3 + - - -
109B SER* 1.3 74.9 - - - +
111B GLU* 1.3 61.7 + - - +
113B GLU* 3.5 26.4 + - - +
114B GLU* 2.8 51.3 + - - +
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Residues in contact with GLU 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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109B SER* 3.2 8.7 + - - +
110B GLN* 1.3 77.0 - - - +
112B GLN* 1.3 63.7 + - + +
114B GLU* 3.4 17.9 + - - +
115B HIS* 2.9 35.9 + - + +
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Residues in contact with GLN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 3.7 10.5 - - + -
108B GLY* 3.6 8.5 - - - -
109B SER* 3.0 37.8 + - - +
111B GLU* 1.3 75.8 - - + +
113B GLU* 1.3 59.2 + - - +
115B HIS* 4.5 4.9 - - + -
116B LEU* 2.8 46.8 + - + +
228B ASP* 2.6 32.2 + - + +
229B GLU 4.0 0.8 - - - -
230B VAL 3.0 27.1 + - - +
231B LEU* 3.9 14.4 - - + +
232B GLY 4.6 0.9 + - - -
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Residues in contact with GLU 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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63B PRO* 5.8 0.7 - - - +
66B TYR* 3.6 17.2 + - - +
104B ILE* 3.4 15.1 - - + +
105B GLU* 3.5 32.2 - - + +
109B SER 2.9 16.3 + - - +
110B GLN* 3.5 28.4 + - - +
112B GLN* 1.3 73.8 - - - +
114B GLU* 1.3 57.8 + - - +
116B LEU* 4.4 0.2 - - - +
117B TYR* 2.8 60.5 + - + +
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Residues in contact with GLU 114 (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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66B TYR* 3.7 34.3 - - + +
110B GLN* 2.8 45.5 + - - +
111B GLU* 3.7 19.4 - - - +
112B GLN 3.3 0.2 - - - -
113B GLU* 1.3 80.4 - - - +
115B HIS* 1.3 57.3 + - - +
118B THR* 2.5 35.3 + - - +
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Residues in contact with HIS 115 (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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111B GLU* 2.9 32.0 + - + +
112B GLN* 4.0 4.9 - - + +
114B GLU* 1.3 73.0 - - - +
116B LEU* 1.3 79.8 + - + +
118B THR* 3.3 4.7 + - - -
119B GLN* 3.1 58.6 + - + +
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Residues in contact with LEU 116 (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 ILE* 4.0 28.0 - - + -
112B GLN* 2.8 31.0 + - + +
115B HIS* 1.3 92.7 - - + +
117B TYR* 1.3 59.1 + - - +
119B GLN* 3.4 2.9 + - + +
120B ILE* 3.0 37.1 + - - +
125B TRP* 4.8 10.1 - - + -
170B LEU* 4.4 23.3 - - + -
191B ALA* 4.0 28.0 - - + +
229B GLU* 6.0 2.0 - - - +
231B LEU* 4.7 8.5 - - + -
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Residues in contact with TYR 117 (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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61B LEU 5.4 1.9 + - - -
62B VAL* 3.6 26.3 - - + +
63B PRO* 3.8 17.0 - - + -
66B TYR* 3.7 38.8 - + + +
101B ALA* 3.8 33.0 - - + -
102B PRO* 3.7 14.4 - - - +
104B ILE* 4.2 7.6 - - + -
105B GLU* 2.7 40.6 + - + +
113B GLU* 2.8 37.9 + - + +
114B GLU 4.2 0.2 - - - +
116B LEU* 1.3 77.8 - - - +
118B THR* 1.3 62.5 + - - +
120B ILE* 3.8 3.5 - - + +
121B ALA* 3.0 26.0 + - - +
327B TRP* 5.3 0.3 - - - -
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Residues in contact with THR 118 (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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66B TYR* 3.7 29.6 - - + +
114B GLU 2.5 25.5 + - - -
115B HIS* 3.6 5.2 - - - -
117B TYR* 1.3 76.4 - - - +
119B GLN* 1.3 61.2 + - - +
121B ALA* 3.8 1.0 - - - +
122B GLN* 2.8 55.4 + - + +
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Residues in contact with GLN 119 (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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115B HIS* 3.1 45.8 + - + +
116B LEU* 3.9 4.9 - - + +
117B TYR 3.3 0.2 - - - -
118B THR* 1.3 80.4 - - - +
120B ILE* 1.3 66.4 + - - +
122B GLN* 3.5 23.1 + - - +
123B ASN* 2.8 54.2 + - - +
125B TRP* 3.5 28.7 - - + -
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Residues in contact with ILE 120 (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 LEU 4.5 11.9 - - - +
59B SER* 4.9 2.8 - - - -
62B VAL* 4.3 16.6 - - + -
97B HIS* 5.0 0.9 - - + -
101B ALA* 3.8 28.7 - - + -
104B ILE* 4.2 8.7 - - + -
116B LEU 3.0 21.4 + - - +
117B TYR* 3.8 7.6 - - + +
119B GLN* 1.3 75.1 - - - +
121B ALA* 1.3 58.2 + - - +
124B ASN* 2.9 26.0 + - - -
125B TRP* 3.2 36.1 + - + +
127B THR* 4.2 13.0 - - + -
170B LEU* 3.9 26.9 - - + -
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Residues in contact with ALA 121 (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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59B SER* 3.8 20.7 + - - -
62B VAL* 4.1 3.8 - - + -
66B TYR 3.3 25.4 - - - +
67B GLY* 3.7 22.3 - - - +
68B GLY 3.8 3.8 - - - +
117B TYR 3.0 12.2 + - - +
120B ILE* 1.3 76.1 - - - +
122B GLN* 1.3 65.3 + - - +
123B ASN 3.5 0.3 + - - -
124B ASN* 3.7 15.8 + - - +
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR 5.7 0.9 - - - +
118B THR* 2.8 37.1 + - + +
119B GLN* 3.5 28.3 + - - +
121B ALA* 1.3 75.0 - - - +
123B ASN* 1.3 69.2 + - - +
124B ASN* 3.5 5.2 + - - -
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Residues in contact with ASN 123 (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 ARG* 5.3 3.5 + - - +
119B GLN* 2.8 51.7 + - - +
122B GLN* 1.3 92.6 + - - +
124B ASN* 1.3 71.9 + - - +
125B TRP* 3.3 38.6 + - + +
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Residues in contact with ASN 124 (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 ARG* 3.6 54.2 - - + +
56B GLY* 3.7 26.0 - - - +
58B LEU* 3.7 13.8 + - + +
59B SER* 4.8 4.9 + - - -
120B ILE 2.9 9.6 + - - -
121B ALA* 3.7 12.9 + - - +
122B GLN 3.5 5.1 + - - -
123B ASN* 1.3 80.1 - - - +
125B TRP* 1.3 63.3 + - - +
126B TRP* 3.7 1.2 + - - -
169B ASP* 4.1 2.9 - - - +
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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