Contacts of the helix formed by residues 201 - 207 (chain C) in PDB entry 1NF3
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 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170C GLY* 4.9 3.8 - - - -
198C VAL* 3.1 22.0 + - - -
199C PRO 3.0 8.2 + - - -
200C GLY* 1.3 82.6 - - - +
202C LEU* 1.3 61.1 - - - -
203C ALA 3.6 1.8 - - - -
204C GLN* 3.6 3.4 + - - -
205C SER* 3.0 27.6 + - - -
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Residues in contact with LEU 202 (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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142C VAL* 3.4 33.4 - - + -
160C LEU* 4.4 19.1 - - + -
161C CYS 4.6 2.7 - - - +
162C LYS* 3.5 39.0 - - + +
163C TYR 5.1 1.8 - - - +
168C PRO 4.1 10.3 + - - +
169C LEU* 3.4 22.5 + - + +
170C GLY* 4.6 1.2 - - - -
201C GLY* 1.3 68.5 - - - -
203C ALA* 1.3 71.8 + - - +
205C SER* 2.7 26.2 + - - +
206C THR* 3.2 12.4 + - + +
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Residues in contact with ALA 203 (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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160C LEU* 4.7 7.0 - - + -
169C LEU 3.0 20.0 + - - +
170C GLY* 3.7 10.1 - - - +
171C PHE* 3.5 28.5 - - + -
197C LEU* 4.3 7.4 - - + -
201C GLY 3.6 0.4 - - - -
202C LEU* 1.3 74.5 - - - +
204C GLN* 1.3 63.0 + - - +
206C THR* 2.8 25.2 + - - -
207C GLY 3.5 3.8 + - - -
208C LEU 4.5 1.7 + - - -
209C LEU* 4.1 17.9 + - + +
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Residues in contact with GLN 204 (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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74A GLN* 4.0 23.2 + - - +
170C GLY 4.7 2.4 + - - -
197C LEU* 4.5 24.5 + - + +
198C VAL 3.7 15.1 + - - +
199C PRO* 3.9 16.3 - - - +
200C GLY* 2.6 31.7 + - - -
201C GLY 3.6 5.4 + - - +
202C LEU 3.2 0.4 - - - -
203C ALA* 1.3 79.8 - - - +
205C SER* 1.3 63.7 + - - +
206C THR 3.2 0.5 + - - -
207C GLY* 3.4 11.8 + - - -
209C LEU 5.4 1.6 - - - -
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Residues in contact with SER 205 (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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5A LYS* 4.6 4.5 + - - +
39A ASN* 5.1 1.9 + - - -
56A PHE* 3.7 19.6 - - - -
74A GLN* 4.5 10.9 - - - +
142C VAL* 5.2 1.4 - - - +
200C GLY 5.3 3.1 - - - -
201C GLY 3.0 16.1 + - - -
202C LEU* 2.7 26.9 + - - +
204C GLN* 1.3 78.6 - - - +
206C THR* 1.3 65.1 + - - +
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Residues in contact with THR 206 (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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5A LYS* 5.2 1.9 + - - -
37A PHE* 3.6 21.1 - - - -
39A ASN* 3.9 11.4 - - - +
56A PHE* 4.0 6.7 - - - -
70A LEU 4.5 2.9 - - - +
142C VAL* 4.3 9.0 - - + -
143C SER* 3.2 36.1 - - - +
160C LEU* 4.1 13.9 - - + +
202C LEU* 3.4 14.4 - - + +
203C ALA* 2.8 18.7 + - - -
205C SER* 1.3 82.6 - - - +
207C GLY* 1.3 58.8 + - - +
208C LEU* 3.2 19.3 + - - +
209C LEU* 4.6 1.6 + - - +
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Residues in contact with GLY 207 (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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70A LEU* 3.8 33.2 - - - +
73A PRO* 6.3 3.8 - - - -
156C ARG* 4.6 0.5 + - - -
203C ALA 3.5 2.2 + - - -
204C GLN* 3.4 13.9 + - - -
206C THR* 1.3 78.2 + - - +
208C LEU* 1.3 63.6 + - - +
209C LEU 3.4 6.2 + - - -
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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