Contacts of the helix formed by residues 156 - 162 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I ASP 2.9 16.9 + - - -
155I GLU* 1.3 74.4 - - - +
157I ALA* 1.3 60.1 + - - -
158I TRP* 3.0 23.1 - - - -
159I ASN* 2.9 22.8 + - - +
172I ARG* 3.2 11.4 - - - -
215I THR* 3.7 4.7 - - - -
216I ALA* 3.7 12.7 - - - +
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Residues in contact with ALA 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I GLU 3.1 2.2 + - - -
156I GLY* 1.3 70.3 - - - -
158I TRP* 1.3 65.1 + - + +
159I ASN 3.1 1.3 + - - -
160I SER* 3.2 24.5 + - - -
172I ARG* 4.3 7.2 - - - +
173I PRO 3.8 9.4 - - - +
174I GLY* 4.1 13.5 - - - -
175I VAL* 4.3 17.3 - - + +
215I THR* 3.1 19.8 + - + +
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Residues in contact with TRP 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE* 3.6 30.1 - - + -
145C SER* 3.7 22.2 - - - +
151I ILE* 3.7 23.7 + - + -
152I ASP* 2.9 30.7 + - - -
153I ASP 4.2 3.4 - - - -
156I GLY* 3.9 12.6 - - - -
157I ALA* 1.3 81.6 - - + +
159I ASN* 1.3 71.2 + - - +
160I SER* 3.2 2.7 - - - -
161I SER* 3.4 19.8 + - - -
162I THR* 4.2 2.8 + - - -
215I THR* 4.3 8.5 - - + -
216I ALA* 3.4 26.9 - - + -
260I MET* 3.8 23.8 - - - -
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Residues in contact with ASN 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152I ASP* 2.9 27.9 + - - +
153I ASP 2.8 28.1 + - - -
156I GLY 2.9 10.5 + - - +
158I TRP* 1.3 87.1 - - - +
160I SER* 1.3 50.9 + - - +
161I SER 2.9 6.5 + - - -
162I THR* 2.6 32.8 + - - +
164I TYR* 3.3 23.6 + - - +
168I ASN* 2.7 31.2 + - - -
172I ARG* 3.6 12.5 + - - +
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Residues in contact with SER 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B GLU* 4.6 4.7 + - - -
138H ILE 4.1 0.9 - - - +
139H ARG* 3.2 9.2 - - - -
140H PHE* 2.7 74.0 + - - -
141H GLY* 4.2 5.2 - - - -
157I ALA 3.2 18.2 + - - -
158I TRP* 4.5 1.7 + - - -
159I ASN* 1.3 77.5 - - - +
161I SER* 1.3 53.7 + - - +
168I ASN* 3.6 4.0 + - - -
172I ARG* 3.7 19.8 - - - +
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Residues in contact with SER 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H ARG* 3.8 14.0 + - - +
140H PHE 3.1 18.3 + - - +
141H GLY* 4.6 3.4 - - - -
148H HIS* 3.4 26.0 + - - -
158I TRP 3.4 15.4 + - - -
160I SER* 1.3 80.5 + - - +
162I THR* 1.3 61.5 + - - +
163I LYS* 3.7 3.5 + - - +
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Residues in contact with THR 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H ARG* 3.3 7.7 - - - +
158I TRP 4.2 3.1 + - - -
159I ASN* 2.6 40.5 + - - +
161I SER* 1.3 79.1 + - - +
163I LYS* 1.3 74.2 + - - +
164I TYR* 3.4 21.6 - - + -
168I ASN* 2.8 24.1 + - - +
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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