Contacts of the strand formed by residues 137 - 143 (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 ASP 137 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G PHE* 3.7 5.3 - - - +
136G ASP* 1.3 83.7 - - + +
138G ILE* 1.3 62.8 + - - +
139G ARG* 2.7 37.7 + - - -
150G ALA 4.7 1.0 - - - +
151G ILE* 3.7 1.4 - - - -
152G ASP* 2.9 49.0 + - + +
252G THR* 4.9 0.2 - - - -
164H TYR 5.1 1.2 + - - -
167H GLY* 3.4 10.5 - - - -
168H ASN* 2.6 39.1 + - - +
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Residues in contact with ILE 138 (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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462A PHE* 3.9 17.0 - - + -
466A TYR* 3.5 52.3 - - + +
135G PHE* 4.8 3.8 - - + -
137G ASP* 1.3 75.1 - - - +
139G ARG* 1.3 64.2 + - - +
140G PHE* 4.0 13.3 - - + -
149G VAL* 4.3 5.8 - - + -
150G ALA 3.6 3.1 - - - +
151G ILE* 3.8 29.2 - - + -
252G THR* 4.2 1.3 - - + +
160H SER 4.0 1.4 - - - +
168H ASN* 2.9 36.3 + - - +
169H LYS 3.6 15.9 - - - +
170H GLY* 3.8 6.6 - - - -
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Residues in contact with ARG 139 (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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137G ASP* 2.7 40.7 + - - -
138G ILE* 1.3 79.0 - - - +
140G PHE* 1.3 65.9 + - - +
148G HIS* 4.3 10.3 + - - +
149G VAL* 3.2 2.8 - - - +
150G ALA* 2.7 64.0 + - + +
152G ASP* 5.5 2.6 - - - +
160H SER 3.2 4.5 - - - +
161H SER* 3.9 12.8 + - - +
162H THR 3.4 26.0 - - - +
163H LYS* 3.7 41.8 - - - +
168H ASN* 3.7 6.5 - - + +
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Residues in contact with PHE 140 (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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459A PRO 4.3 3.4 - - - +
462A PHE* 3.6 38.4 - + + -
463A GLU* 3.4 37.5 - - + -
466A TYR* 4.3 9.2 - + + -
138G ILE* 4.0 22.4 - - + -
139G ARG* 1.3 79.8 - - - +
141G GLY* 1.3 62.2 + - - +
148G HIS* 3.1 24.1 + - - +
149G VAL* 4.0 5.4 - - + -
160H SER* 2.8 61.8 + - - -
161H SER* 3.2 2.9 + - - -
170H GLY* 4.7 15.9 - - - -
172H ARG* 6.3 1.1 - - + -
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Residues in contact with GLY 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A PRO* 4.3 4.2 + - - +
463A GLU* 4.1 11.9 - - - -
140G PHE* 1.3 79.0 - - - +
142G ALA* 1.3 62.3 + - - +
147G SER* 3.2 4.0 - - - -
148G HIS* 2.9 42.8 + - - +
160H SER* 4.3 3.1 - - - -
161H SER* 4.7 3.1 - - - -
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Residues in contact with ALA 142 (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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460A VAL* 4.0 28.0 - - + -
463A GLU* 3.9 17.4 + - - +
141G GLY* 1.3 75.6 - - - +
143G SER* 1.3 62.7 + - - +
146G GLY 3.4 9.4 - - - +
147G SER* 4.2 5.8 - - - -
452G ARG* 4.4 6.8 + - - +
456G THR* 4.9 6.1 - - + -
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Residues in contact with SER 143 (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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261A PHE* 5.2 7.3 + - - +
142G ALA* 1.3 75.0 - - - +
144G ILE* 1.3 67.7 + - - +
145G SER* 3.2 20.6 + - - -
146G GLY 2.8 21.9 + - - +
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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