Contacts of the strand formed by residues 146 - 152 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D ALA* 3.4 1.9 - - - +
143D SER* 2.8 37.5 + - - +
144D ILE 3.4 1.8 + - - -
145D SER* 1.3 82.0 + - - +
147D SER* 1.3 62.8 + - - -
456D THR* 6.1 0.2 - - - +
149J VAL* 3.2 19.7 - - - -
150J ALA* 4.7 0.2 - - - -
151J ILE* 5.6 1.1 - - - -
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Residues in contact with SER 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D GLY 3.2 13.0 - - - -
142D ALA* 4.2 8.5 - - - -
146D GLY* 1.3 76.4 - - - -
148D HIS* 1.3 69.1 + - - +
456D THR* 4.6 7.2 - - - +
457D PRO 3.5 21.5 + - - -
459D PRO* 4.2 2.8 - - - +
148J HIS* 3.3 0.7 - - - -
149J VAL* 2.9 40.5 + - - +
459J PRO* 3.6 20.9 - - - -
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Residues in contact with HIS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C SER* 3.5 38.3 + - - -
139D ARG* 4.3 11.5 + - + +
140D PHE* 3.1 15.0 + - - +
141D GLY* 2.9 47.6 + - - +
147D SER* 1.3 80.8 - - - +
149D VAL* 1.3 68.1 + - - +
150D ALA* 4.6 5.4 - - + -
147J SER 3.3 7.6 - - - +
148J HIS* 3.4 18.4 - - + -
459J PRO* 3.6 10.9 - - - +
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ILE* 4.3 7.9 - - + -
139D ARG 3.2 10.8 - - - +
140D PHE* 4.1 3.8 - - + -
148D HIS* 1.3 77.5 - - - +
150D ALA* 1.3 66.6 + - - +
151D ILE* 4.5 4.7 - - + -
146J GLY* 3.2 9.3 - - - -
147J SER* 2.9 47.7 + - - +
457J PRO* 5.0 1.6 - - + +
459J PRO* 4.3 8.5 - - + -
462J PHE* 3.7 54.7 - - + -
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASP 3.9 1.0 - - - +
138D ILE* 3.6 4.7 + - - +
139D ARG* 2.7 69.2 + - + +
148D HIS* 4.6 5.4 - - + -
149D VAL* 1.3 75.4 - - - +
151D ILE* 1.3 62.7 + - - +
152D ASP* 5.5 0.2 - - - -
145J SER 3.7 3.4 - - - -
146J GLY* 4.7 0.2 - - - -
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Residues in contact with ILE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D PHE* 3.6 37.0 - - + -
137D ASP 3.8 3.1 - - - -
138D ILE* 3.8 19.7 - - + -
149D VAL* 4.5 5.2 - - + -
150D ALA* 1.3 74.7 - - - +
152D ASP* 1.3 71.0 + - - +
158D TRP* 3.7 15.5 + - + -
259D PRO* 3.5 36.1 - - + +
260D MET* 3.7 18.4 - - + -
145J SER* 2.8 39.0 + - - +
146J GLY* 5.6 0.7 - - - -
462J PHE* 4.4 6.5 - - + -
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Residues in contact with ASP 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D PHE* 3.6 1.9 - - - +
136D ASP* 2.9 23.8 + - + -
137D ASP* 2.9 39.3 + - + +
139D ARG* 5.5 1.8 - - - +
151D ILE* 1.3 80.7 - - - +
153D ASP* 1.3 63.2 + - - +
158D TRP* 2.9 25.8 + - - -
159D ASN* 2.9 21.0 + - - +
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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