Contacts of the helix formed by residues 156 - 170 (chain C) in PDB entry 1VF6
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 156 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLN 2.9 10.2 + - - +
153C LEU* 3.1 19.0 + - + +
155C GLN* 1.3 77.5 - - - +
157C ARG* 1.3 65.1 + - - +
158C ASP* 2.8 38.5 + - - +
159C PHE* 2.9 14.7 + - + +
160C GLN* 3.0 22.9 + - - +
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Residues in contact with ARG 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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155C GLN 3.5 3.7 + - - -
156C ASN* 1.3 74.2 + - - +
158C ASP* 1.3 63.1 + - - +
160C GLN* 3.4 8.9 + - + +
161C ASN* 2.9 53.2 + - - +
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Residues in contact with ASP 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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51A LEU* 4.1 8.3 - - + +
54A GLN* 4.2 3.2 + - + +
55A GLN* 2.7 33.2 + - - +
58A LYS* 2.8 36.4 + - - +
156C ASN* 2.8 21.8 + - - +
157C ARG* 1.3 76.7 - - - +
159C PHE* 1.3 63.2 + - - +
161C ASN* 3.4 12.6 + - - +
162C ALA* 3.2 22.3 + - - +
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Residues in contact with PHE 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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38A PHE* 3.9 30.1 - + - -
41A THR* 6.1 0.2 - - + -
42A LEU* 4.1 7.0 - - + -
47A PHE* 3.9 25.4 - + - -
51A LEU* 4.6 9.8 - - + +
124C VAL* 5.6 0.7 - - + -
127C LEU* 4.2 3.8 - - + -
153C LEU* 3.3 48.7 - - + +
154C VAL* 3.7 26.7 - - + -
156C ASN* 2.9 11.1 + - - +
158C ASP* 1.3 76.1 - - - +
160C GLN* 1.3 57.8 + - + +
162C ALA* 3.2 4.3 + - - +
163C PHE* 2.8 72.5 + + + +
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Residues in contact with GLN 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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124C VAL* 4.0 27.3 - - + +
154C VAL 2.9 29.3 + - - +
155C GLN* 3.6 23.3 + - - +
156C ASN 3.0 12.8 + - - +
157C ARG* 3.7 8.4 - - + +
159C PHE* 1.3 88.0 - - + +
161C ASN* 1.3 59.1 + - - +
163C PHE* 4.1 3.6 - - - -
164C LYS* 2.9 57.4 + - - +
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Residues in contact with ASN 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 3.8 17.3 - - - +
157C ARG* 2.9 47.0 + - - +
158C ASP* 3.8 10.9 + - - +
159C PHE 3.3 0.4 - - - -
160C GLN* 1.3 77.5 - - - +
162C ALA* 1.3 62.8 + - - +
164C LYS* 4.1 11.2 - - - +
165C ILE* 3.1 31.4 + - + +
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Residues in contact with ALA 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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47A PHE* 3.7 13.5 - - + -
50A ILE* 3.9 15.4 - - + +
51A LEU* 3.6 31.9 - - + -
54A GLN* 3.3 20.8 - - - +
158C ASP 3.2 2.7 + - - +
159C PHE 3.2 5.3 + - - +
161C ASN* 1.3 78.3 - - - +
163C PHE* 1.3 57.8 + - - +
165C ILE* 3.8 1.4 - - - +
166C HIS* 2.9 32.1 + - - +
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Residues in contact with PHE 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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38A PHE* 5.0 5.4 - + - -
41A THR* 4.3 29.4 - - + -
47A PHE* 3.7 6.4 - + - -
123C ASP* 3.8 31.0 - - + -
124C VAL* 3.9 21.8 - - + -
127C LEU* 4.1 20.2 - - + -
159C PHE* 2.8 46.5 + + + +
160C GLN* 3.6 4.5 - - - +
162C ALA* 1.3 77.7 - - - +
164C LYS* 1.3 61.7 + - - +
166C HIS* 3.4 2.5 + - - +
167C ASN* 3.0 54.9 + - - -
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Residues in contact with LYS 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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121C ASP* 3.0 49.1 - - + +
124C VAL* 3.6 15.3 - - + +
160C GLN* 2.9 44.6 + - - +
161C ASN* 4.1 11.7 - - - +
163C PHE* 1.3 76.0 - - - +
165C ILE* 1.3 61.2 + - + +
167C ASN* 3.3 6.8 + - - +
168C ALA* 2.8 32.0 + - - +
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Residues in contact with ILE 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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50A ILE* 3.9 10.3 - - + -
54A GLN* 2.8 31.4 - - - +
64B LEU* 5.0 9.9 - - + -
68B LEU* 3.8 39.0 - - + -
161C ASN* 3.1 15.6 + - + +
162C ALA 3.8 3.6 - - - +
164C LYS* 1.3 73.0 - - + +
166C HIS* 1.3 67.4 + - - +
168C ALA* 3.3 6.0 + - - +
169C VAL* 3.0 31.0 + - + +
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Residues in contact with HIS 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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41A THR* 3.8 24.3 + - + +
44A SER* 3.2 31.2 + - - -
46A LEU* 3.6 30.3 - - + +
47A PHE* 3.6 20.6 + + + -
50A ILE* 3.9 11.2 - - + +
162C ALA 2.9 18.8 + - - +
163C PHE 3.5 3.6 - - - +
165C ILE* 1.3 77.1 - - - +
167C ASN* 1.3 77.8 + - - +
169C VAL* 3.1 11.1 + - - +
170C THR* 3.2 32.0 + - + +
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Residues in contact with ASN 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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41A THR* 5.2 2.1 + - - +
121C ASP* 6.1 0.2 - - - +
123C ASP* 3.6 28.4 + - - +
163C PHE* 3.0 57.9 + - - +
164C LYS* 3.8 5.8 - - - +
166C HIS* 1.3 86.8 - - - +
168C ALA* 1.3 60.6 + - - +
169C VAL 3.0 6.2 + - - -
170C THR* 3.2 23.9 + - - +
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Residues in contact with ALA 168 (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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164C LYS 2.8 21.9 + - - +
165C ILE* 3.8 7.4 - - - +
166C HIS 3.3 0.4 - - - -
167C ASN* 1.3 72.4 - - - +
169C VAL* 1.3 62.6 + - + +
170C THR 3.5 0.4 - - - -
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Residues in contact with VAL 169 (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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46A LEU* 4.5 13.0 - - + -
68B LEU* 4.3 34.3 - - + +
69B GLU* 3.3 44.5 - - + +
165C ILE* 3.0 21.3 - - + +
166C HIS* 3.1 4.9 + - - +
167C ASN 3.0 1.2 - - - -
168C ALA* 1.3 83.4 - - + +
170C THR* 1.3 60.0 + - - +
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Residues in contact with THR 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.9 21.3 - - + -
69B GLU* 6.0 0.4 - - - +
166C HIS* 3.2 31.4 + - + +
167C ASN* 3.2 20.7 + - - +
168C ALA 3.5 0.4 - - - -
169C VAL* 1.3 85.8 - - + +
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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