Contacts of the helix formed by residues 109 - 123 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104H ILE 4.7 1.0 - - - +
105H GLU* 5.5 0.2 - - - -
108H GLY* 1.3 75.7 - - - +
110H GLN* 1.3 60.7 + - - +
111H GLU* 3.5 6.3 + - - +
112H GLN* 2.8 34.9 + - - +
113H GLU* 3.0 29.8 + - - +
232H GLY 5.3 0.4 - - - +
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Residues in contact with GLN 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H TYR* 4.6 4.4 + - - -
109H SER* 1.3 74.6 - - - +
111H GLU* 1.3 65.1 + - - +
113H GLU* 3.5 18.7 + - - +
114H GLU* 2.7 58.3 + - - +
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Residues in contact with GLU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H SER* 3.5 5.6 + - - +
110H GLN* 1.3 78.7 - - - +
112H GLN* 1.3 65.2 + - + +
114H GLU* 3.7 20.9 + - - +
115H HIS* 3.1 56.2 + - + +
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Residues in contact with GLN 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ILE* 3.9 6.5 - - + -
108H GLY* 3.6 8.3 - - - -
109H SER* 2.8 38.3 + - - +
110H GLN 3.3 0.4 - - - -
111H GLU* 1.3 77.4 - - + +
113H GLU* 1.3 70.0 + - - +
115H HIS* 5.1 1.6 - - - -
116H LEU* 2.9 43.2 + - + +
227H PRO 4.7 0.8 + - - -
228H ASP* 2.8 32.0 + - - +
229H GLU 4.2 2.0 - - - -
230H VAL 2.8 27.8 + - - +
231H LEU* 3.9 8.3 - - + +
232H GLY 4.8 1.2 + - - -
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Residues in contact with GLU 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H PRO* 5.9 1.4 - - - +
65H GLU* 5.6 0.7 - - - +
66H TYR* 4.2 22.3 + - + +
104H ILE* 3.6 12.9 - - + +
105H GLU* 3.7 38.6 - - + +
108H GLY 5.6 0.2 - - - +
109H SER 3.0 20.4 + - - +
110H GLN* 3.5 24.9 + - - +
112H GLN* 1.3 78.4 - - - +
114H GLU* 1.3 63.0 + - - +
117H TYR* 3.1 36.7 + - + +
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Residues in contact with GLU 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H TYR* 3.0 35.5 - - + +
110H GLN* 2.7 44.1 + - - +
111H GLU* 3.9 24.0 - - - +
112H GLN 3.3 0.8 - - - -
113H GLU* 1.3 80.4 - - - +
115H HIS* 1.3 61.0 + - + +
118H THR* 2.5 33.1 + - - -
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Residues in contact with HIS 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H GLU* 3.1 40.7 + - + +
112H GLN* 4.4 1.6 - - - +
113H GLU 3.3 0.2 - - - -
114H GLU* 1.3 80.7 + - + +
116H LEU* 1.3 67.7 + - + +
118H THR* 3.6 7.6 + - - +
119H GLN* 3.3 32.0 + - + +
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Residues in contact with LEU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ILE* 3.7 23.1 - - + -
112H GLN* 2.9 42.1 + - + +
115H HIS* 1.3 71.2 - - + +
117H TYR* 1.3 64.9 + - - +
119H GLN* 3.5 3.4 + - - +
120H ILE* 3.1 32.2 + - + +
125H TRP* 5.9 0.6 - - + -
170H LEU* 4.7 15.9 - - + +
191H ALA* 4.4 25.8 - - + +
228H ASP 5.6 1.8 - - - +
229H GLU* 5.7 4.0 - - + +
231H LEU* 4.1 19.1 - - + -
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Residues in contact with TYR 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H LEU 4.2 7.3 + - - -
62H VAL* 3.4 36.6 - - + +
63H PRO* 3.4 23.6 - - + -
66H TYR* 4.0 18.4 - + + -
101H ALA* 4.0 10.3 - - + +
102H PRO* 3.4 27.9 - - - +
104H ILE* 3.6 38.6 - - + -
105H GLU* 3.6 24.4 + - + +
113H GLU* 3.1 31.9 + - + +
116H LEU* 1.3 75.5 - - - +
118H THR* 1.3 57.5 + - - +
120H ILE* 3.2 10.2 + - + +
121H ALA* 2.9 31.9 + - - +
327H TRP* 5.4 0.9 - - - -
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Residues in contact with THR 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H TYR* 3.0 28.9 - - - +
114H GLU 2.5 24.4 + - - -
115H HIS* 3.8 9.4 - - - +
116H LEU 3.3 0.4 - - - -
117H TYR* 1.3 77.7 - - - +
119H GLN* 1.3 72.5 + - + +
121H ALA* 3.5 1.2 + - - +
122H GLN* 2.9 57.7 + - - +
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Residues in contact with GLN 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H HIS* 3.3 21.4 + - + +
116H LEU* 3.9 2.9 - - - +
118H THR* 1.3 89.9 - - + +
120H ILE* 1.3 63.1 + - - +
122H GLN* 2.7 29.7 + - - +
123H ASN* 2.7 49.9 + - - +
125H TRP* 3.6 24.7 - - + -
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Residues in contact with ILE 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H LEU 4.6 9.9 - - - +
59H SER* 4.9 2.7 - - - -
62H VAL* 4.2 17.7 - - + -
97H HIS* 5.1 0.9 - - + -
101H ALA* 5.3 9.6 - - + -
104H ILE* 4.0 16.8 - - + -
116H LEU 3.1 27.2 + - - +
117H TYR* 3.5 10.5 - - + +
119H GLN* 1.3 77.6 - - - +
121H ALA* 1.3 58.5 + - - +
124H ASN* 3.2 9.5 + - - -
125H TRP* 3.0 48.3 + - + +
127H THR* 4.3 19.3 - - + -
170H LEU* 3.7 29.6 - - + -
172H PHE* 4.7 1.3 - - + -
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Residues in contact with ALA 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H SER* 3.9 18.2 + - - -
62H VAL* 3.9 11.4 - - + -
66H TYR 3.3 26.0 - - - +
67H GLY* 3.7 23.6 - - - +
117H TYR 2.9 12.8 + - - +
118H THR 4.1 0.2 - - - +
120H ILE* 1.3 76.2 - - - +
122H GLN* 1.3 60.8 + - - +
124H ASN* 3.8 14.2 - - - +
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Residues in contact with GLN 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H TYR 5.1 6.4 + - - +
67H GLY* 6.3 0.9 - - - -
118H THR* 2.9 32.5 + - - +
119H GLN* 2.7 36.1 + - - +
121H ALA* 1.3 79.1 - - - +
123H ASN* 1.3 64.0 + - - +
124H ASN* 3.4 6.5 + - - -
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Residues in contact with ASN 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H ARG* 4.5 4.9 + - - -
119H GLN* 2.7 52.0 + - - +
122H GLN* 1.3 80.1 - - - +
124H ASN* 1.3 69.2 + - - +
125H TRP* 3.1 38.7 - - + +
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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