Contacts of the helix formed by residues 105 - 120 (chain H) in PDB entry 1GZ0
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 ASP 105 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H VAL* 3.5 4.0 - - - +
104H THR* 1.3 79.1 + - - +
106H PRO* 1.3 73.4 - - - +
107H HIS* 2.8 30.4 + - - +
108H ASN* 2.9 39.0 + - - +
109H LEU* 3.0 9.5 + - - +
132H ALA* 3.7 1.1 - - - -
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Residues in contact with PRO 106 (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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104H THR 3.5 7.9 - - - +
105H ASP* 1.3 89.4 - - - +
107H HIS* 1.3 62.3 + - - +
109H LEU* 3.3 4.4 + - + +
110H GLY 2.9 19.4 + - - -
132H ALA* 3.4 14.0 - - + -
133H GLN 3.8 8.7 - - - +
135H ASN* 3.1 43.5 - - - +
137H THR* 4.6 8.3 - - + -
138H ALA* 3.4 14.7 - - + +
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Residues in contact with HIS 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C HIS* 5.3 15.0 + + - -
105H ASP* 2.8 19.0 + - - +
106H PRO* 1.3 83.1 - - - +
108H ASN* 1.3 70.7 + - - +
110H GLY 3.2 0.5 + - - -
111H ALA* 3.0 22.4 + - + +
137H THR* 4.3 16.1 - - + +
141H VAL* 3.4 43.3 - - + +
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Residues in contact with ASN 108 (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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103H VAL* 3.6 15.5 - - + +
105H ASP* 2.9 31.9 + - - +
107H HIS* 1.3 81.7 + - - +
109H LEU* 1.3 67.0 + - - +
111H ALA* 2.9 8.7 + - - +
112H CYS* 2.9 27.3 + - - -
198H GLU* 6.3 0.6 - - - +
226H ASN* 4.5 14.7 + - - +
227H VAL* 3.8 27.0 - - + +
228H SER* 4.9 2.6 + - - -
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Residues in contact with LEU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H LEU* 3.9 22.4 - - + -
103H VAL* 3.6 12.2 - - + +
105H ASP 3.0 11.6 + - - +
106H PRO* 3.5 10.3 - - + +
108H ASN* 1.3 75.6 - - - +
110H GLY* 1.3 61.7 + - - +
112H CYS* 3.5 4.2 + - - +
113H LEU* 3.1 26.7 + - + +
126H VAL* 4.8 5.2 - - + -
131H SER* 4.9 4.0 - - - +
132H ALA* 3.6 28.7 - - + +
133H GLN 3.7 19.7 - - - +
134H LEU* 4.1 4.9 - - + +
138H ALA* 4.5 4.5 - - + -
151H LEU* 4.0 35.7 - - + -
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Residues in contact with GLY 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H PRO 2.9 12.6 + - - -
107H HIS 3.7 3.6 - - - -
109H LEU* 1.3 74.9 - - - +
111H ALA* 1.3 59.2 + - - +
113H LEU* 3.1 5.8 + - - +
114H ARG 2.9 24.3 + - - -
138H ALA* 3.3 28.2 - - - +
141H VAL* 4.0 2.7 - - - -
142H ALA* 3.3 19.0 - - - -
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Residues in contact with ALA 111 (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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226C ASN* 6.2 3.8 - - + -
229C VAL* 5.6 2.6 - - + +
107H HIS* 3.0 18.9 + - + +
108H ASN* 2.9 11.3 + - - +
110H GLY* 1.3 75.5 - - - +
112H CYS* 1.3 62.4 + - - +
114H ARG* 3.2 9.3 + - - +
115H SER* 3.1 24.3 + - - -
141H VAL* 3.6 12.9 - - + +
228H SER* 3.4 27.1 - - - +
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Residues in contact with CYS 112 (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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98H LEU* 4.2 5.2 - - + +
100H LEU* 3.8 35.7 - - + -
103H VAL* 5.0 2.5 - - - -
108H ASN 2.9 21.4 + - - +
109H LEU 3.9 0.9 - - - +
111H ALA* 1.3 76.5 - - - +
113H LEU* 1.3 58.6 + - - +
115H SER* 3.4 6.7 + - - +
116H ALA* 2.8 30.6 + - - +
227H VAL* 4.2 10.5 - - - -
228H SER* 4.1 17.0 - - - -
231H THR* 3.7 28.3 - - + +
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Residues in contact with LEU 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H LEU* 6.1 0.4 - - + -
109H LEU* 3.1 27.2 + - + +
110H GLY* 3.1 14.9 + - - +
112H CYS* 1.3 74.7 - - + +
114H ARG* 1.3 65.4 + - - +
116H ALA* 3.0 4.1 + - - +
117H ASP* 2.9 25.6 + - - +
124H VAL* 3.8 30.5 - - + -
134H LEU* 3.8 29.8 - - + -
142H ALA* 4.1 7.4 - - + -
145H ALA* 3.6 6.6 - - + +
146H ALA* 4.5 13.9 - - + -
149H VAL* 4.0 26.1 - - + +
151H LEU* 4.5 11.0 - - + -
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Residues in contact with ARG 114 (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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198C GLU* 2.9 35.5 + - - +
224C SER* 2.5 51.7 + - - +
225C LEU* 3.6 5.7 + - - -
226C ASN* 3.4 34.8 - - - +
110H GLY 2.9 12.2 + - - +
111H ALA* 3.2 11.4 + - - +
113H LEU* 1.3 77.5 - - - +
115H SER* 1.3 63.9 + - - +
117H ASP* 3.3 5.7 + - - +
118H ALA* 3.0 21.8 + - - +
141H VAL 3.8 16.9 + - - +
142H ALA* 3.7 11.4 - - - +
143H CYS* 3.6 28.9 - - + +
145H ALA* 3.8 11.6 - - + +
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Residues in contact with SER 115 (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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225C LEU* 3.7 18.3 - - - +
229C VAL* 3.5 26.9 - - - +
111H ALA 3.1 11.6 + - - -
112H CYS* 3.8 9.0 - - - -
114H ARG* 1.3 77.5 - - - +
116H ALA* 1.3 64.2 + - - +
118H ALA* 3.1 3.6 + - - +
119H ALA* 2.9 25.1 + - - +
228H SER 4.4 3.0 + - - -
231H THR* 5.0 0.4 - - - -
232H GLY* 4.2 19.7 - - - -
235H LEU* 4.2 8.7 - - - -
236H PHE* 4.1 2.6 - - - -
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Residues in contact with ALA 116 (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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98H LEU* 4.1 9.4 - - + -
112H CYS 2.8 22.4 + - - +
113H LEU* 3.3 6.7 - - - +
115H SER* 1.3 74.4 - - - +
117H ASP* 1.3 63.2 + - - +
119H ALA* 3.1 2.9 + - - -
120H GLY 3.1 17.7 + - - -
121H VAL* 3.1 22.5 + - + +
124H VAL* 4.0 25.8 - - + -
149H VAL* 4.5 3.6 - - + -
235H LEU* 4.0 11.1 - - - +
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Residues in contact with ASP 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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219C ALA* 3.8 5.7 - - - +
220C GLY* 4.5 1.7 + - - -
223C SER* 3.4 23.2 + - - -
224C SER 4.5 1.0 + - - +
17H ARG* 2.9 43.2 + - - -
113H LEU 2.9 12.1 + - - +
114H ARG* 3.4 9.9 - - - +
116H ALA* 1.3 76.5 - - - +
118H ALA* 1.3 62.2 + - - +
120H GLY* 3.1 12.9 + - - +
121H VAL 5.1 0.7 - - - +
145H ALA* 3.6 15.1 - - + +
148H SER* 4.0 9.0 - - - -
149H VAL* 3.6 17.1 - - + +
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Residues in contact with ALA 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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217C PRO 3.9 1.2 - - - +
218C MSE 3.7 24.8 - - - -
219C ALA 2.9 24.0 + - - -
223C SER* 3.6 15.0 - - - -
224C SER 4.5 3.4 - - - +
225C LEU* 3.6 26.0 - - + -
114H ARG 3.0 11.3 + - - +
115H SER 3.5 7.4 - - - +
117H ASP* 1.3 76.6 - - - +
119H ALA* 1.3 58.9 + - - +
236H PHE* 3.8 8.5 - - + -
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Residues in contact with ALA 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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219C ALA* 3.8 4.6 - - - +
96H PHE* 3.3 19.0 - - + -
115H SER 2.9 14.9 + - - +
116H ALA 3.1 4.9 + - - +
118H ALA* 1.3 77.5 - - - +
120H GLY* 1.3 60.6 + - - +
121H VAL* 4.6 0.7 - - + -
235H LEU* 3.8 22.2 - - + -
236H PHE* 3.7 21.1 - - + -
239H VAL* 3.7 21.2 - - + +
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Residues in contact with GLY 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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219C ALA* 3.3 19.6 - - - +
96H PHE* 3.6 12.0 - - - -
116H ALA 3.1 3.0 + - - -
117H ASP 3.1 8.1 + - - -
119H ALA* 1.3 80.2 - - - +
121H VAL* 1.3 65.2 + - - +
122H HIS* 3.6 14.9 + - - -
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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