Contacts of the helix formed by residues 155 - 167 (chain C) in PDB entry 2GD4
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 ASN 155 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C THR 3.7 1.2 + - - -
154C PHE* 1.3 78.4 - - - +
156C GLU* 1.3 77.1 + - - +
157C THR* 2.6 17.0 + - - -
158C TYR* 3.9 14.9 - - + +
159C GLN* 3.1 24.4 + - - +
353C GLY 3.3 21.2 + - - +
354C ILE* 3.1 13.5 + - - +
355C VAL* 4.5 2.8 - - - +
1E NAG 1.4 63.6 + - - +
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Residues in contact with GLU 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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154C PHE 3.6 1.5 + - - -
155C ASN* 1.3 79.1 + - - +
157C THR* 1.3 67.5 + - - +
159C GLN* 3.2 8.8 - - - +
160C ASP* 2.9 28.0 + - - +
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Residues in contact with THR 157 (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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16C PRO* 5.2 14.8 - - + -
155C ASN* 2.6 16.7 + - - -
156C GLU* 1.3 70.4 - - - +
158C TYR* 1.3 58.9 + - - +
160C ASP* 2.4 40.2 + - + +
161C ILE* 2.8 27.5 + - + -
1E NAG 3.7 32.5 - - - -
2E NAG 5.3 4.5 - - + +
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Residues in contact with TYR 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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89C MET* 2.7 36.0 + - + +
92C LEU* 3.4 30.1 - - + -
93C GLY* 4.6 3.8 - - - -
146C LEU* 2.9 29.1 - - + +
154C PHE* 6.0 0.4 - - + -
155C ASN* 3.8 22.2 + - + -
157C THR* 1.3 78.8 - - - +
159C GLN* 1.3 68.8 + - + +
161C ILE* 3.0 10.3 + - + +
162C SER* 2.6 54.2 + - - -
170C LEU* 4.9 4.3 - - + -
353C GLY 4.1 8.3 - - - +
354C ILE* 3.6 40.5 - - + +
1E NAG 4.6 0.8 + - - +
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Residues in contact with GLN 159 (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 PHE* 4.6 11.9 - - + +
155C ASN 3.1 18.8 + - - +
156C GLU* 3.2 13.0 + - - +
157C THR 2.8 1.6 + - - -
158C TYR* 1.3 87.4 - - + +
160C ASP* 1.3 64.5 + - - +
162C SER* 4.3 1.5 - - - -
163C GLU* 3.2 21.1 + - - +
169C LYS* 3.1 21.4 - - + +
170C LEU* 2.6 62.5 + - - +
172C PRO* 5.1 3.6 - - - +
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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
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16C PRO* 5.5 9.2 - - + -
156C GLU* 2.9 25.6 + - - +
157C THR* 2.4 30.1 + - + +
159C GLN* 1.3 67.0 - - - +
161C ILE* 1.3 67.9 - - + +
163C GLU* 3.1 6.6 + - - +
164C LEU* 3.1 28.9 - - + +
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Residues in contact with ILE 161 (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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15C ILE* 6.3 1.6 - - + -
16C PRO* 4.6 22.0 - - + +
17C MET* 6.3 0.4 - - - -
19C PRO* 5.1 9.2 - - + -
89C MET* 5.3 0.2 - - - -
92C LEU* 3.7 39.9 - - + -
120C HIS* 4.0 26.0 - - + +
157C THR* 2.8 31.2 + - + +
158C TYR* 3.3 10.3 - - + +
160C ASP* 1.3 78.8 - - + +
162C SER* 1.3 57.0 + - - +
163C GLU 2.5 14.7 + - - -
164C LEU* 2.9 12.1 + - - -
165C VAL* 3.2 24.0 + - + +
1E NAG 5.4 1.3 - - - +
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Residues in contact with SER 162 (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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89C MET* 5.0 5.7 - - - +
92C LEU* 5.1 0.4 - - - +
146C LEU* 5.8 3.1 - - - +
158C TYR* 2.6 44.8 + - - -
159C GLN* 4.0 7.0 - - - -
161C ILE* 1.3 75.5 - - - +
163C GLU* 1.3 59.6 + - - +
165C VAL* 4.8 0.4 - - - -
166C TYR* 3.2 32.8 + - - +
167C GLY 3.3 1.7 + - - -
168C ALA 2.7 30.4 + - - +
169C LYS* 3.7 9.1 + - - -
170C LEU 4.3 0.3 + - - -
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Residues in contact with GLU 163 (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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159C GLN 3.2 14.6 + - - +
160C ASP* 3.1 10.6 + - - +
161C ILE 2.5 6.1 + - - -
162C SER* 1.3 72.3 - - - +
164C LEU* 1.3 76.1 + - + +
165C VAL 3.0 0.2 - - - -
167C GLY* 2.8 44.5 + - - +
168C ALA* 3.6 13.2 + - - -
169C LYS* 4.2 8.8 + - + +
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Residues in contact with LEU 164 (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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4C PRO 4.1 6.1 - - - +
5C VAL* 3.8 40.2 - - + -
7C ILE* 2.9 25.2 - - + +
15C ILE* 5.5 8.7 - - + -
121C PHE* 5.9 0.2 - - - -
160C ASP* 3.1 21.8 - - + +
161C ILE* 2.9 5.3 + - - +
163C GLU* 1.3 93.1 - - + +
165C VAL* 1.3 66.5 + - + +
167C GLY* 5.5 0.2 - - - -
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Residues in contact with VAL 165 (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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7C ILE* 4.8 1.9 - - + +
15C ILE* 6.0 5.6 - - + -
85C THR* 6.2 0.2 - - - +
89C MET* 3.8 15.3 - - + +
120C HIS* 3.1 45.1 - - + +
121C PHE* 4.1 16.2 - - + -
124C ALA* 3.3 24.1 - - + +
127C ASN* 5.9 0.2 + - - -
161C ILE* 3.5 29.2 - - + +
162C SER* 4.8 0.7 - - - +
163C GLU 2.9 2.8 + - - -
164C LEU* 1.3 85.9 - - + +
166C TYR* 1.3 63.6 + - - +
167C GLY 3.3 1.1 - - - -
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Residues in contact with TYR 166 (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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85C THR* 4.4 17.7 - - + -
86C ALA* 3.6 37.3 - - + +
89C MET* 3.6 32.5 - - + -
144C ASN* 3.3 64.8 + - - +
145C ARG* 3.8 18.7 - - + -
146C LEU* 4.3 12.7 - - + +
162C SER* 3.2 22.5 + - - +
165C VAL* 1.3 79.3 - - - +
167C GLY* 1.3 58.4 + - - +
168C ALA 3.6 5.8 + - - -
169C LYS 6.0 0.2 - - - -
216C VAL 4.0 4.5 + - - -
217C ASN* 4.1 1.6 + - - +
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Residues in contact with GLY 167 (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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162C SER 3.3 0.2 + - - -
163C GLU* 2.8 26.5 + - - +
164C LEU 5.5 0.2 - - - -
165C VAL 3.3 2.0 - - - -
166C TYR* 1.3 80.4 - - - +
168C ALA* 1.3 58.4 + - - +
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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