Contacts of the strand formed by residues 146 - 152 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A VAL* 3.3 19.7 - - - -
150A ALA* 4.8 0.2 - - - -
151A ILE* 5.6 1.3 - - - -
259A PRO 6.2 0.2 - - - -
142G ALA* 3.4 1.6 - - - +
143G SER* 2.8 39.2 + - - +
144G ILE 3.4 1.8 + - - -
145G SER* 1.3 81.8 + - - +
147G SER* 1.3 63.5 + - - -
456G THR* 6.1 0.3 - - - +
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Residues in contact with SER 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A HIS* 3.4 0.5 - - - -
149A VAL* 3.0 39.3 + - - +
458A HIS* 5.1 0.9 - - - -
459A PRO* 3.7 20.0 - - - -
141G GLY 3.2 13.7 - - - -
142G ALA* 4.2 9.0 - - - -
146G GLY* 1.3 76.5 - - - -
148G HIS* 1.3 69.1 + - - +
456G THR* 4.6 6.2 - - - +
457G PRO 3.5 21.2 + - - -
459G PRO* 4.2 3.3 - - - +
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Residues in contact with HIS 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER 3.4 7.4 - - - +
148A HIS* 3.5 17.7 - - + -
459A PRO* 3.6 10.5 - - - +
139G ARG* 4.3 11.9 + - + +
140G PHE* 3.1 15.8 + - - +
141G GLY* 2.9 47.4 + - - +
147G SER* 1.3 81.0 - - - +
149G VAL* 1.3 67.1 - - - +
150G ALA* 4.6 5.6 - - + -
161H SER* 3.5 36.5 + - - -
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Residues in contact with VAL 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY* 3.3 8.8 - - - -
147A SER* 3.0 44.8 + - - +
457A PRO* 5.0 1.3 - - + +
459A PRO* 4.1 10.1 - - + -
462A PHE* 3.6 54.7 - - + -
138G ILE* 4.3 7.0 - - + -
139G ARG 3.2 12.1 - - - +
140G PHE* 4.1 3.6 - - + -
148G HIS* 1.3 77.9 - - - +
150G ALA* 1.3 66.1 + - - +
151G ILE* 4.5 4.3 - - + -
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Residues in contact with ALA 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A SER 3.8 3.4 - - - -
146A GLY* 4.8 0.2 - - - -
137G ASP 3.9 1.4 - - - +
138G ILE* 3.6 3.8 - - - +
139G ARG* 2.7 69.8 + - + +
148G HIS* 5.0 4.9 - - + -
149G VAL* 1.3 75.8 - - - +
151G ILE* 1.3 65.0 + - - +
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Residues in contact with ILE 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A SER* 2.9 29.8 + - - +
146A GLY* 5.6 0.9 - - - -
462A PHE* 4.2 7.2 - - + -
135G PHE* 3.6 36.6 - - + -
137G ASP 3.8 3.1 - - - -
138G ILE* 3.8 21.3 - - + -
149G VAL* 4.5 4.9 - - + -
150G ALA* 1.3 74.3 - - - +
152G ASP* 1.3 70.7 + - - +
158G TRP* 3.7 22.9 + - + -
259G PRO* 3.5 36.8 - - + +
260G MET* 3.7 16.6 - - + -
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Residues in contact with ASP 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G PHE* 3.6 1.7 - - - +
136G ASP* 2.9 24.5 + - + -
137G ASP* 2.9 39.2 + - + +
139G ARG* 5.5 2.0 - - - +
151G ILE* 1.3 81.7 - - - +
153G ASP* 1.3 62.3 + - - +
158G TRP* 2.9 25.5 + - - -
159G ASN* 2.9 21.7 + - - +
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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