Contacts of the helix formed by residues 156 - 162 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153K ASP 2.9 16.5 + - - -
155K GLU* 1.3 75.2 - - - +
157K ALA* 1.3 60.9 + - - -
158K TRP* 3.0 22.4 - - - -
159K ASN* 2.9 23.2 + - - +
172K ARG* 3.2 11.6 - - - -
215K THR* 3.7 5.2 - - - -
216K ALA* 3.7 13.1 - - - +
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Residues in contact with ALA 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155K GLU 4.0 1.8 - - - -
156K GLY* 1.3 71.0 - - - -
158K TRP* 1.3 65.3 + - + +
159K ASN 3.1 1.3 + - - -
160K SER* 3.2 24.2 + - - -
172K ARG* 4.3 7.0 - - - +
173K PRO 3.8 10.1 - - - +
174K GLY* 4.1 13.7 - - - -
175K VAL* 4.3 17.0 - - + +
215K THR* 3.1 20.4 + - + +
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Residues in contact with TRP 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E ILE* 3.6 32.3 - - + -
145E SER* 3.7 23.5 - - - +
151K ILE* 3.7 23.7 + - + -
152K ASP* 2.9 31.1 + - - -
153K ASP 4.2 1.6 - - - -
156K GLY* 3.9 13.5 - - - -
157K ALA* 1.3 83.1 - - + +
159K ASN* 1.3 70.3 + - - +
160K SER* 3.2 2.6 + - - -
161K SER* 3.4 19.6 + - - -
162K THR* 4.2 2.8 + - - -
215K THR* 4.3 7.9 - - + -
216K ALA* 3.4 28.0 - - + -
260K MET* 3.8 24.7 - - - -
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Residues in contact with ASN 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152K ASP* 2.9 27.6 + - - +
153K ASP 2.8 27.7 + - - -
156K GLY 2.9 10.7 + - - +
158K TRP* 1.3 87.9 - - - +
160K SER* 1.3 49.3 + - - +
161K SER 2.9 6.6 + - - -
162K THR* 2.6 32.1 + - - +
164K TYR* 3.3 24.9 + - - +
168K ASN* 2.7 31.2 + - - -
172K ARG* 3.6 11.2 + - - +
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Residues in contact with SER 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D GLU* 4.8 3.8 + - - -
138J ILE 4.0 1.6 - - - +
139J ARG* 3.2 9.5 - - - -
140J PHE* 2.8 68.7 + - - -
141J GLY* 4.3 4.5 - - - -
157K ALA 3.2 18.1 + - - -
158K TRP 3.2 1.9 + - - -
159K ASN* 1.3 77.0 - - - +
161K SER* 1.3 57.4 + - - +
168K ASN* 3.6 5.0 + - - -
170K GLY* 5.9 0.2 - - - -
172K ARG* 3.7 18.6 - - - +
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Residues in contact with SER 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J ARG* 3.8 13.7 + - - +
140J PHE 3.4 16.8 - - - +
141J GLY* 4.7 2.5 - - - -
148J HIS* 3.5 25.1 + - - -
158K TRP 3.4 15.1 + - - -
160K SER* 1.3 80.4 + - - +
162K THR* 1.3 61.2 + - - +
163K LYS* 3.7 3.6 + - - +
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Residues in contact with THR 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J ARG* 3.4 7.2 - - - +
158K TRP 4.2 2.8 + - - -
159K ASN* 2.6 41.1 + - - +
161K SER* 1.3 79.1 + - - +
163K LYS* 1.3 75.8 + - - +
164K TYR* 3.4 21.3 - - + -
168K ASN* 2.8 24.9 + - - +
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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