Contacts of the strand formed by residues 146 - 152 (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 146 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C VAL* 3.2 19.3 - - - -
150C ALA* 4.7 0.2 - - - -
151C ILE* 5.6 1.1 - - - -
259C PRO 6.2 0.2 - - - -
142I ALA* 3.4 1.7 - - - +
143I SER* 2.8 38.9 + - - +
144I ILE 3.4 1.6 + - - -
145I SER* 1.3 81.6 + - - +
147I SER* 1.3 63.8 + - - -
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Residues in contact with SER 147 (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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148C HIS* 3.3 0.9 - - - +
149C VAL* 2.9 41.2 + - - +
458C HIS* 5.1 0.9 - - - -
459C PRO* 3.7 20.4 - - - -
141I GLY 3.2 13.5 - - - -
142I ALA* 4.1 9.0 - - - +
146I GLY* 1.3 74.6 - - - -
148I HIS* 1.3 68.7 + - - +
456I THR* 4.6 6.3 - - - +
457I PRO 3.5 21.2 + - - -
459I PRO* 4.2 3.2 - - - +
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Residues in contact with HIS 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C SER 3.3 7.6 - - - -
148C HIS* 3.4 18.4 - - + -
459C PRO* 3.6 10.0 - - - +
139I ARG* 4.3 11.5 + - + +
140I PHE* 3.1 15.0 + - - +
141I GLY* 2.9 47.8 + - - +
147I SER* 1.3 82.3 - - - +
149I VAL* 1.3 68.0 + - - +
150I ALA* 4.6 5.6 - - + -
161J SER* 3.4 37.3 + - - -
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Residues in contact with VAL 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C GLY* 3.2 9.5 - - - -
147C SER* 2.9 48.5 + - - +
457C PRO* 5.0 1.1 - - + +
459C PRO* 4.2 9.0 - - + -
462C PHE* 3.7 54.3 - - + -
138I ILE* 4.3 7.6 - - + -
139I ARG 3.2 11.7 - - - +
140I PHE* 4.1 3.8 - - + -
148I HIS* 1.3 77.7 - - - +
150I ALA* 1.3 66.7 + - - +
151I ILE* 4.5 5.2 - - + -
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Residues in contact with ALA 150 (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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145C SER 3.7 2.9 - - - -
146C GLY* 4.7 0.2 - - - -
137I ASP 3.9 1.4 - - - +
138I ILE* 3.6 4.0 - - - +
139I ARG* 2.7 69.6 + - + +
148I HIS* 5.0 4.9 - - + -
149I VAL* 1.3 75.8 - - - +
151I ILE* 1.3 64.8 + - - +
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Residues in contact with ILE 151 (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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145C SER* 2.8 40.1 + - - +
146C GLY* 5.5 0.4 - - - -
462C PHE* 4.4 6.7 - - + -
135I PHE* 3.6 36.8 - - + -
137I ASP 3.8 3.1 - - - -
138I ILE* 3.8 20.4 - - + -
149I VAL* 4.5 5.2 - - + -
150I ALA* 1.3 75.0 - - - +
152I ASP* 1.3 70.9 + - - +
158I TRP* 3.7 15.1 + - + -
259I PRO* 3.5 36.6 - - + +
260I MET* 3.7 17.0 - - + -
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Residues in contact with ASP 152 (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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135I PHE* 3.6 2.3 - - - +
136I ASP* 2.9 23.8 + - + -
137I ASP* 2.9 38.5 + - + +
139I ARG* 5.5 2.2 - - - +
151I ILE* 1.3 82.3 - - - +
153I ASP* 1.3 61.7 + - - +
158I TRP* 2.9 26.1 + - - -
159I ASN* 2.9 22.0 + - - +
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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