Contacts of the helix formed by residues 156 - 162 (chain L) in PDB entry 1F1H
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 156 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153L ASP 2.9 15.2 + - - -
155L GLU* 1.3 75.0 - - - +
157L ALA* 1.3 60.0 + - - -
158L TRP* 3.0 23.3 - - - -
159L ASN* 2.9 22.5 + - - +
172L ARG* 3.2 11.0 - - - -
215L THR* 3.7 5.2 - - - -
216L ALA* 3.7 13.5 - - - +
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Residues in contact with ALA 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L GLU 3.1 2.4 + - - -
156L GLY* 1.3 70.6 - - - -
158L TRP* 1.3 64.9 + - + +
159L ASN 3.1 2.2 + - - -
160L SER* 3.2 24.0 + - - -
172L ARG* 4.3 7.0 - - - +
173L PRO 3.8 10.1 - - - +
174L GLY* 4.1 13.0 - - - -
175L VAL* 4.3 17.5 - - + +
215L THR* 3.1 19.4 + - + +
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Residues in contact with TRP 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F ILE* 3.7 30.1 - - + -
145F SER* 3.7 23.3 - - - +
151L ILE* 3.7 23.9 + - + -
152L ASP* 2.9 30.6 + - - -
153L ASP 4.2 3.6 - - - -
156L GLY* 3.9 13.5 - - - -
157L ALA* 1.3 82.0 - - + +
159L ASN* 1.3 71.9 + - - +
160L SER* 3.2 3.3 + - - -
161L SER* 3.4 19.4 + - - -
162L THR* 4.2 2.8 + - - -
215L THR* 4.3 7.4 - - + -
216L ALA* 3.4 26.7 - - + -
260L MET* 3.8 24.9 - - - -
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Residues in contact with ASN 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L ASP* 2.9 28.5 + - - +
153L ASP 2.8 28.1 + - - -
156L GLY 2.9 10.9 + - - +
158L TRP* 1.3 86.6 - - - +
160L SER* 1.3 49.4 + - - +
161L SER 2.9 6.8 + - - -
162L THR* 2.6 32.5 + - - +
164L TYR* 3.3 22.2 + - - +
168L ASN* 2.7 30.5 + - - -
172L ARG* 3.6 12.4 + - - +
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Residues in contact with SER 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463E GLU* 4.5 4.7 + - - -
138K ILE 4.1 1.0 - - - +
139K ARG* 3.3 8.7 - - - -
140K PHE* 2.8 72.5 + - - -
141K GLY* 4.3 5.2 - - - -
157L ALA 3.2 18.8 + - - -
158L TRP 3.2 1.9 + - - -
159L ASN* 1.3 76.3 - - - +
161L SER* 1.3 53.8 + - - +
168L ASN* 3.6 4.4 + - - -
170L GLY* 5.9 0.4 - - - -
172L ARG* 3.7 18.5 - - - +
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Residues in contact with SER 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K ARG* 3.9 13.8 + - - +
140K PHE 3.1 17.4 + - - +
141K GLY* 4.5 3.1 - - - -
148K HIS* 3.5 26.2 + - - -
158L TRP 3.4 14.9 + - - -
160L SER* 1.3 81.1 + - - +
162L THR* 1.3 62.4 + - - +
163L LYS* 3.7 3.5 + - - +
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Residues in contact with THR 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K ARG* 3.3 7.9 - - - +
158L TRP 4.2 2.8 + - - -
159L ASN* 2.6 40.4 + - - +
161L SER* 1.3 78.2 + - - +
163L LYS* 1.3 76.4 + - - +
164L TYR* 3.4 21.9 - - + -
168L ASN* 2.8 24.4 + - - +
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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