Contacts of the helix formed by residues 131 - 144 (chain H) in PDB entry 3ECS
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 131 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H HIS 5.5 3.4 - - - -
129H ALA 4.2 0.6 + - - -
130H TYR* 1.3 79.0 - - - +
132H ARG* 1.3 58.9 + - - +
133H VAL* 3.8 0.9 - - - +
134H VAL* 3.0 34.5 + - - +
135H LEU* 2.9 26.2 + - - +
164H MSE 3.9 7.1 - - - +
195H VAL* 6.0 0.2 - - - -
196H GLY* 3.8 16.9 - - - -
508H SO4 2.7 26.5 + - - -
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Residues in contact with ARG 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H MSE 6.2 0.6 - - - -
18H PRO 2.6 31.3 + - - -
19H ASP* 3.7 25.6 - - - +
20H MSE 3.5 12.8 + - - -
21H ALA* 4.1 3.2 - - - +
22H SER* 4.0 20.8 - - - +
108H ARG* 3.7 22.9 - - - +
130H TYR* 4.0 24.3 - - + +
131H SER* 1.3 72.3 - - - +
133H VAL* 1.3 56.8 + - - +
135H LEU* 3.6 11.0 - - + +
136H ARG* 3.1 31.4 + - - +
508H SO4 2.9 33.2 + - - +
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Residues in contact with VAL 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H ARG* 4.3 22.4 - - + +
111H ILE* 4.3 22.4 - - + -
131H SER* 3.0 3.1 - - - +
132H ARG* 1.3 77.4 - - - +
134H VAL* 1.3 61.5 + - - +
136H ARG* 3.6 2.6 + - - +
137H VAL* 3.0 29.7 + - + +
229H VAL* 3.6 33.2 - - + +
230H ALA 4.5 0.2 - - - +
231H GLU* 3.4 32.8 - - - +
234H LYS* 4.2 0.4 - - - +
508H SO4 3.0 21.8 - - - +
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Residues in contact with VAL 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H ILE* 6.3 0.2 - - + -
127H THR* 4.0 18.4 - - - +
131H SER* 3.0 27.8 + - - +
133H VAL* 1.3 76.0 - - - +
135H LEU* 1.3 65.1 + - - +
137H VAL* 3.2 6.9 + - + +
138H LEU* 3.1 34.1 + - + +
164H MSE 4.0 14.6 - - + -
194H ILE* 4.1 20.6 - - + +
195H VAL* 3.8 4.7 - - - -
196H GLY 3.7 13.0 - - - +
229H VAL* 3.5 21.8 - - + -
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Residues in contact with LEU 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ASP* 5.9 3.4 - - - +
130H TYR* 3.6 24.2 - - + +
131H SER 2.9 12.5 + - - +
132H ARG* 3.6 13.2 - - + +
133H VAL 3.3 0.4 - - - -
134H VAL* 1.3 78.2 - - - +
136H ARG* 1.3 56.6 + - - +
138H LEU* 3.3 2.9 + - - -
139H GLU* 2.9 53.1 + - + +
164H MSE 4.0 20.1 - - + +
167H ALA* 4.0 18.2 - - + -
168H LEU* 4.4 12.3 - - + -
171H LEU* 3.7 17.5 - - + -
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Residues in contact with ARG 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ASP* 3.9 15.8 + - - -
105H SER 5.4 5.9 + - - -
108H ARG* 3.4 58.3 - - + +
109H ASN* 2.8 36.7 + - - +
112H ALA* 3.7 12.2 - - + +
132H ARG 3.1 12.9 + - - +
133H VAL 3.9 5.4 - - - +
134H VAL 3.3 0.2 - - - -
135H LEU* 1.3 75.2 - - - +
137H VAL* 1.3 58.4 + - - +
139H GLU* 3.6 20.7 + - - +
140H ALA* 2.9 30.3 + - - +
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Residues in contact with VAL 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H ARG 5.4 0.2 - - - +
111H ILE* 4.4 6.5 - - + -
112H ALA* 3.8 31.3 - - + +
115H CYS* 4.0 18.8 - - - -
116H HIS* 6.1 0.5 - - - -
119H ILE* 3.5 23.2 - - + +
133H VAL* 3.0 22.0 - - + +
134H VAL* 3.2 12.9 + - + +
136H ARG* 1.3 76.9 - - - +
138H LEU* 1.3 58.9 + - + +
140H ALA* 3.5 3.6 - - - +
141H ALA* 3.1 23.7 + - - +
194H ILE* 5.2 7.0 - - + -
229H VAL* 4.3 19.3 - - + -
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Residues in contact with LEU 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H ILE* 3.8 22.0 - - + -
125H ILE* 3.9 17.7 - - + -
127H THR* 5.8 2.5 - - + -
134H VAL* 3.1 33.1 + - + +
135H LEU 3.9 3.1 - - - +
137H VAL* 1.3 77.0 - - + +
139H GLU* 1.3 56.2 + - - +
140H ALA 3.2 0.2 - - - -
141H ALA* 3.0 4.7 + - - +
142H VAL* 2.7 41.1 + - + +
148H PHE* 3.7 28.4 - - + -
150H VAL* 4.5 10.8 - - + -
164H MSE 4.5 6.3 - - + -
168H LEU* 3.9 30.7 - - + -
171H LEU* 5.7 0.4 - - - -
194H ILE* 4.8 5.2 - - + -
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Residues in contact with GLU 139 (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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135H LEU* 2.9 57.3 + - + +
136H ARG* 3.6 24.1 + - - +
138H LEU* 1.3 75.1 - - - +
140H ALA* 1.3 62.9 + - - +
142H VAL* 2.7 31.4 - - + +
143H ALA* 2.9 10.0 + - - +
171H LEU* 3.6 18.7 - - + +
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Residues in contact with ALA 140 (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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112H ALA* 4.0 23.1 - - + +
113H ASP* 4.3 13.5 - - - +
116H HIS* 6.0 3.1 - - + -
136H ARG 2.9 19.0 + - - +
137H VAL 3.5 6.3 - - - +
139H GLU* 1.3 78.5 - - - +
141H ALA* 1.3 57.5 + - - +
143H ALA* 3.2 6.7 + - - +
144H ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H HIS* 5.9 7.8 - - + +
119H ILE* 3.9 27.6 - - + -
137H VAL 3.1 10.8 + - - +
138H LEU 3.0 10.0 + - - +
140H ALA* 1.3 80.7 - - - +
142H VAL* 1.3 59.8 + - - +
144H ALA* 3.3 13.8 + - - +
145H LYS 3.3 0.2 + - - -
146H LYS* 3.0 29.9 + - + +
148H PHE* 3.8 17.0 - - + -
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Residues in contact with VAL 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H LEU 2.7 20.0 + - - +
139H GLU* 2.7 34.3 - - + +
141H ALA* 1.3 67.8 - - - +
143H ALA* 1.3 64.4 + - + +
144H ALA 3.0 1.3 - - - -
145H LYS* 2.6 35.2 + - - +
146H LYS 4.4 8.1 - - - +
148H PHE* 3.6 22.2 - - + -
171H LEU* 3.8 21.5 - - + +
173H VAL* 3.7 23.6 - - + -
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Residues in contact with ALA 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H GLU 2.9 8.4 + - - +
140H ALA* 3.6 10.3 - - - +
142H VAL* 1.3 84.3 - - + +
144H ALA* 1.3 58.4 + - - +
145H LYS* 3.0 26.5 + - - +
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Residues in contact with ALA 144 (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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116H HIS* 5.9 9.0 - - + -
140H ALA 2.9 13.7 + - - +
141H ALA* 3.4 14.6 - - - +
142H VAL 3.0 0.6 - - - -
143H ALA* 1.3 73.3 - - - +
145H LYS* 1.3 68.8 + - - +
146H LYS* 3.4 15.2 + - + +
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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