Contacts of the helix formed by residues 157 - 167 (chain F) in PDB entry 6V3O
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 157 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B GLU* 6.2 0.2 - - - -
155F GLY 3.9 1.2 + - - -
156F LYS* 1.3 76.5 - - - +
158F PRO* 1.3 71.1 - - - +
159F GLU* 3.4 17.3 + - - +
160F GLU* 3.0 45.0 + - - +
161F VAL* 3.1 13.2 + - - +
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Residues in contact with PRO 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F VAL* 3.8 25.8 - - + -
156F LYS 3.9 0.2 - - - -
157F SER* 1.3 86.9 - - - +
159F GLU* 1.3 65.1 + - - +
161F VAL* 3.4 9.1 + - + +
162F PHE* 2.9 30.8 + - - +
270F ILE* 3.5 31.7 - - + +
271F GLY 5.3 1.1 - - - -
272F ILE* 3.9 20.8 - - + +
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Residues in contact with GLU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F SER* 3.4 19.2 + - - +
158F PRO* 1.3 84.3 - - - +
160F GLU* 1.3 58.7 + - + +
162F PHE* 3.4 4.8 + - - +
163F GLU* 2.9 29.7 + - - +
272F ILE* 4.3 17.5 - - + +
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Residues in contact with GLU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B SER* 5.2 9.4 - - - -
160B GLU* 6.2 0.3 - - - -
156F LYS* 3.4 32.8 + - + +
157F SER* 3.0 30.8 + - - +
159F GLU* 1.3 73.4 - - + +
161F VAL* 1.3 54.3 + - - +
163F GLU* 3.2 6.2 + - - +
164F ALA* 2.7 36.7 + - - +
703F MET* 4.8 6.0 - - - +
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Residues in contact with VAL 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F LEU* 3.6 32.3 - - + -
150F LEU* 4.3 11.4 - - + -
151F VAL* 4.1 20.4 - - + -
156F LYS* 4.3 14.6 - - + -
157F SER 3.1 14.3 + - - +
158F PRO* 3.6 7.6 - - + +
160F GLU* 1.3 75.4 - - - +
162F PHE* 1.3 63.3 + - - +
164F ALA* 3.0 9.2 + - - +
165F LEU* 3.0 27.9 + - + +
267F LEU* 5.0 0.4 - - + -
270F ILE* 4.5 9.9 - - + -
699F LEU* 4.3 10.5 - - + +
703F MET* 4.4 9.4 - - + -
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Residues in contact with PHE 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F PRO 2.9 18.5 + - - +
159F GLU* 3.7 6.3 - - - +
161F VAL* 1.3 76.6 - - - +
163F GLU* 1.3 61.0 + - + +
165F LEU* 3.6 3.4 + - + +
166F LYS* 3.3 52.0 + - - +
267F LEU* 3.7 39.0 - - + +
272F ILE* 4.1 26.2 - - + -
274F GLU* 3.8 33.9 - - + -
275F ARG 4.0 17.0 - - - -
276F LEU* 4.2 15.3 - - + -
277F PRO* 4.1 6.1 - - + -
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Residues in contact with GLU 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F GLU 2.9 18.0 + - - +
160F GLU* 3.8 5.6 - - - +
162F PHE* 1.3 75.0 - - + +
164F ALA* 1.3 60.2 + - - +
166F LYS* 3.3 33.7 + - - +
167F ASN* 2.4 54.1 + - - +
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Residues in contact with ALA 164 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160F GLU 2.7 21.4 + - - +
161F VAL 3.3 5.4 - - - +
163F GLU* 1.3 74.3 - - - +
165F LEU* 1.3 61.9 + - - +
167F ASN* 3.2 14.9 + - - +
168F GLN* 3.3 13.5 + - - +
666F GLY* 5.8 0.9 - - - -
699F LEU* 3.7 18.6 - - + +
703F MET* 3.9 17.3 - - + -
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Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F ILE* 5.2 3.4 - - + -
147F LEU* 4.6 6.1 - - + -
161F VAL* 3.0 20.8 + - + +
162F PHE 3.9 4.9 - - - +
163F GLU 3.3 0.2 - - - -
164F ALA* 1.3 76.9 - - - +
166F LYS* 1.3 62.2 + - - +
168F GLN* 3.2 15.7 + - - +
263F VAL* 4.4 18.4 - - + -
267F LEU* 3.9 29.2 - - + -
276F LEU* 4.2 14.0 - - + +
280F VAL* 5.1 2.4 - - - +
282F LEU* 3.4 39.8 - - + +
695F THR* 4.3 15.9 - - + -
699F LEU* 4.0 31.0 - - + -
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Residues in contact with LYS 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F PHE* 3.3 47.1 + - + +
163F GLU* 3.3 33.1 + - - +
164F ALA 3.3 0.8 - - - -
165F LEU* 1.3 77.3 - - - +
167F ASN* 1.3 63.4 + - - +
168F GLN 3.4 2.5 + - - +
274F GLU* 5.1 2.4 + - - -
276F LEU* 4.4 13.0 - - + -
277F PRO* 4.4 17.1 - - + +
280F VAL* 4.1 27.4 - - + +
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Residues in contact with ASN 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F GLU* 2.4 55.5 + - - +
164F ALA* 3.2 8.7 + - - +
165F LEU 3.1 0.4 - - - -
166F LYS* 1.3 80.4 - - - +
168F GLN* 1.3 60.1 + - - +
169F THR* 4.0 2.5 + - - -
634F LYS* 5.6 3.1 + - - -
665F ASN 5.0 1.4 - - - +
666F GLY* 3.6 13.0 - - - +
667F SER* 5.6 0.5 - - - -
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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
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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