Contacts of the helix formed by residues 143 - 161 (chain C) in PDB entry 5EIB
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 GLY 143 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ASN* 4.0 5.6 - - - -
140C SER* 3.3 6.8 + - - -
142C GLY* 1.3 76.5 - - - +
144C GLY* 1.3 55.6 + - - -
145C THR 3.3 2.7 - - - -
146C GLY 4.1 0.4 - - - -
147C SER* 2.6 37.6 + - - -
186C ASN* 4.1 0.9 - - - -
501C GTP 3.2 38.3 + - - -
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Residues in contact with GLY 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ALA* 3.5 11.2 - - - -
101C ASN* 3.6 4.6 - - - +
102C ASN 3.4 35.1 - - - +
103C TYR 3.9 0.2 - - - -
106C GLY* 3.5 7.6 - - - -
143C GLY* 1.3 73.2 - - - -
145C THR* 1.3 57.0 + - - +
147C SER* 3.5 2.0 + - - -
148C GLY* 2.8 27.5 + - - -
501C GTP 3.0 10.9 + - - -
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Residues in contact with THR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.7 20.2 - - + +
10C GLY* 3.7 13.0 - - - +
68C VAL* 5.5 0.4 - - + -
69C ASP* 3.9 12.2 + - - +
70C LEU* 3.3 34.3 - - + +
99C ALA* 3.7 1.5 - - - +
144C GLY* 1.3 74.9 - - - +
146C GLY* 1.3 66.9 + - - +
147C SER 3.1 1.1 - - - -
149C PHE* 2.9 40.3 + - + +
150C THR 3.4 2.9 + - - -
501C GTP 2.7 31.6 + - - -
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Residues in contact with GLY 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 4.1 6.5 - - - -
139C HIS* 2.9 22.7 + - - -
140C SER* 3.0 22.2 - - - -
143C GLY 3.9 1.0 + - - -
145C THR* 1.3 72.5 - - - +
147C SER* 1.3 56.6 - - - +
150C THR* 2.6 26.4 + - - -
501C GTP 2.8 21.4 + - - -
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Residues in contact with SER 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 3.7 13.7 - - - -
140C SER 3.4 2.6 + - - -
141C PHE 3.3 20.2 - - - -
143C GLY 2.6 24.2 + - - -
144C GLY 3.5 2.3 + - - -
146C GLY* 1.3 77.8 - - - +
148C GLY* 1.3 70.3 + - - +
150C THR 4.1 0.2 - - - -
151C SER* 3.2 14.9 + - - -
186C ASN* 3.5 26.9 - - - +
190C THR* 2.9 27.6 + - - -
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Residues in contact with GLY 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 3.4 32.3 - - - -
106C GLY 3.5 7.2 - - - -
107C HIS* 3.3 11.1 + - - -
144C GLY 2.8 20.2 + - - -
147C SER* 1.3 74.3 + - - +
149C PHE* 1.3 64.7 + - - +
151C SER* 3.0 14.2 + - - -
152C LEU 3.3 6.8 + - - -
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Residues in contact with PHE 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.8 17.5 - - + -
68C VAL* 4.1 18.4 - - + -
70C LEU* 4.4 7.9 - - + -
106C GLY* 3.4 12.8 + - - +
111C GLY* 3.6 28.7 - - - -
114C ILE* 3.6 22.0 - - + -
115C ILE* 3.7 25.1 - - + -
118C VAL* 3.8 23.8 - - + -
144C GLY 3.6 1.4 + - - -
145C THR* 2.9 27.8 + - + +
148C GLY* 1.3 76.2 - - - +
150C THR* 1.3 57.9 + - - +
152C LEU* 3.2 6.0 + - + +
153C LEU* 2.8 45.1 + - + +
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Residues in contact with THR 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.5 14.4 - - - +
137C VAL* 4.0 12.8 - - + -
139C HIS* 3.3 41.0 - - + +
145C THR 3.4 1.4 + - - -
146C GLY 2.6 27.8 + - - -
147C SER 4.0 1.8 - - - -
148C GLY 3.3 0.6 - - - -
149C PHE* 1.3 79.9 - - - +
151C SER* 1.3 58.6 + - - +
153C LEU* 3.2 6.9 + - + +
154C MET* 2.7 48.5 + - + +
168C GLU* 4.8 2.5 - - - +
190C THR* 4.8 0.7 - - - +
194C THR* 5.0 2.7 - - - +
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Residues in contact with SER 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C TYR* 3.2 10.0 + - - -
107C HIS* 3.2 14.2 + - - -
147C SER 3.2 13.0 + - - -
148C GLY 3.0 13.5 + - - -
150C THR* 1.3 79.7 - - - +
152C LEU* 1.3 56.7 + - - +
154C MET* 3.9 2.5 - - - +
155C GLU* 3.0 34.0 + - - +
190C THR* 3.8 2.9 - - - -
193C THR* 3.1 26.3 - - - +
194C THR* 3.5 20.0 - - - -
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Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLY 4.4 0.7 - - - +
107C HIS* 3.6 26.2 - - + +
111C GLY 3.9 18.2 - - - -
112C LYS* 3.3 32.5 - - + +
115C ILE* 3.7 34.1 - - + -
148C GLY 3.3 9.6 + - - +
149C PHE* 3.2 14.5 + - + +
151C SER* 1.3 79.7 + - - +
153C LEU* 1.3 63.7 + - - +
155C GLU* 3.5 14.1 + - - +
156C ARG* 3.1 40.5 + - + +
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.6 36.6 - - + -
9C VAL* 4.3 13.0 - - + -
68C VAL* 5.8 0.2 - - + -
115C ILE* 4.1 11.0 - - + +
118C VAL* 4.2 11.0 - - + -
119C LEU* 4.1 13.2 - - + -
122C ILE* 4.0 16.8 - - + -
137C VAL* 5.3 6.1 - - + -
149C PHE* 2.8 30.0 + - + +
150C THR* 3.5 5.8 - - - +
152C LEU* 1.3 78.2 - - - +
154C MET* 1.3 52.9 + - + +
156C ARG* 3.3 1.7 + - - -
157C LEU* 2.8 58.3 + - + +
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Residues in contact with MET 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C VAL* 3.9 28.7 - - + -
150C THR* 2.7 40.0 + - + +
151C SER* 3.9 5.8 - - - +
153C LEU* 1.3 71.2 - - + +
155C GLU* 1.3 64.6 + - - +
157C LEU* 3.4 6.2 + - - -
158C SER* 3.0 25.8 + - - -
166C LYS* 3.7 35.3 - - + -
168C GLU* 3.9 13.0 - - + -
194C THR* 3.7 27.6 - - + +
197C HIS* 4.0 14.0 - - + +
198C SER* 3.8 21.3 - - - +
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Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C HIS* 3.4 29.3 + - - -
112C LYS* 5.5 0.2 + - - -
151C SER 3.0 20.5 + - - +
152C LEU* 3.6 12.7 - - - +
154C MET* 1.3 75.2 - - - +
156C ARG* 1.3 64.1 + - + +
158C SER* 3.1 13.5 + - - -
159C VAL* 3.3 16.4 + - - +
193C THR* 4.4 16.3 - - - +
197C HIS* 3.8 30.6 + - + +
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Residues in contact with ARG 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ILE* 3.9 27.1 - - + +
116C ASP* 3.2 26.7 + - - -
119C LEU* 3.2 35.9 - - + +
152C LEU* 3.1 26.9 + - + +
153C LEU* 3.8 4.3 - - - +
155C GLU* 1.3 78.3 - - + +
157C LEU* 1.3 66.0 + - - +
159C VAL* 3.2 9.9 + - - +
160C ASP* 3.0 37.6 + - - -
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.7 26.7 - - + -
119C LEU* 3.8 19.5 - - + -
122C ILE* 4.3 9.6 - - + -
135C PHE* 4.1 23.3 - - + -
137C VAL* 5.1 0.9 - - + -
153C LEU* 2.8 37.1 + - + +
154C MET* 3.9 10.1 - - - +
156C ARG* 1.3 73.2 - - - +
158C SER* 1.3 56.9 + - - +
160C ASP* 4.7 0.2 - - - -
161C TYR* 2.8 64.0 + - + +
166C LYS* 4.0 18.5 + - + +
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Residues in contact with SER 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C MET 3.0 6.9 + - - -
155C GLU 3.3 8.1 - - - -
156C ARG 3.1 0.4 - - - -
157C LEU* 1.3 75.3 - - - +
159C VAL* 1.3 63.6 + - - +
161C TYR 4.9 0.2 - - - -
162C GLY* 3.4 24.2 - - - -
166C LYS* 2.9 25.6 + - - +
197C HIS* 2.9 37.1 + - - +
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Residues in contact with VAL 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C GLU 3.3 12.5 + - - +
156C ARG* 3.2 13.1 + - - +
158C SER* 1.3 78.9 - - - +
160C ASP* 1.3 72.6 + - - +
162C GLY 4.5 2.4 + - - -
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Residues in contact with ASP 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 4.2 24.1 - - + +
123C ARG* 3.8 17.8 + - - +
156C ARG* 3.0 26.4 + - - +
157C LEU* 3.3 0.6 + - - -
159C VAL* 1.3 93.4 - - - +
161C TYR* 1.3 83.4 + - + +
162C GLY 3.9 0.9 - - - -
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Residues in contact with TYR 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 4.8 4.1 + - + -
122C ILE* 3.8 4.4 - - + +
123C ARG* 3.1 60.8 + - - -
126C ALA* 3.6 18.5 - - + +
132C LEU* 4.2 6.1 - - + -
135C PHE* 3.9 25.8 - + + -
157C LEU* 2.8 41.5 + - + +
158C SER* 4.9 1.0 - - - -
160C ASP* 1.3 95.1 - - + +
162C GLY* 1.3 64.2 + - - +
163C LYS 3.2 2.9 - - - -
164C LYS* 3.0 45.2 + - + +
166C LYS* 5.3 3.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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