Contacts of the strand formed by residues 123 - 135 (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 THR 123 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G GLU* 5.1 2.9 - - - +
115G LEU* 3.9 3.9 - - - +
116G ARG* 5.0 5.2 - - - +
121G ALA 3.8 0.4 - - - -
122G ASP* 1.3 99.6 + - + +
124G VAL* 1.3 62.8 + - - +
125G LEU* 4.2 13.9 + - - +
227G THR* 4.7 15.7 - - + -
274G LEU* 3.7 5.7 - - - +
275G ALA* 3.1 40.4 + - - +
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Residues in contact with VAL 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G GLU* 3.4 24.6 + - + +
115G LEU* 3.7 19.5 - - + -
123G THR* 1.3 74.0 - - - +
125G LEU* 1.3 64.7 + - - +
126G PHE* 3.9 14.8 - - + -
227G THR* 3.2 8.0 - - - -
228G MET* 3.0 31.8 + - + -
272G MET* 6.0 1.1 - - + -
273G SER 3.9 2.9 - - - +
274G LEU* 3.3 22.0 - - + -
297G TYR* 4.7 3.6 - - + +
375G LEU* 3.7 35.2 - - + -
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Residues in contact with LEU 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G THR* 4.2 10.0 + - - +
124G VAL* 1.3 85.2 - - - +
126G PHE* 1.3 65.1 + - - +
225G PHE* 3.6 32.5 - - + -
226G ASN 3.7 2.0 - - - +
227G THR* 4.2 21.8 - - + +
271G HIS 4.4 0.4 - - - -
272G MET* 3.2 25.8 - - - +
273G SER* 2.9 34.7 + - - +
275G ALA* 5.0 14.4 - - + -
1477G ADP 4.1 13.9 - - - +
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Residues in contact with PHE 126 (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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124G VAL* 3.9 17.3 - - + -
125G LEU* 1.3 79.8 - - - +
127G GLY* 1.3 59.6 + - - +
128G PRO* 3.9 2.0 - - + -
225G PHE* 3.1 5.3 - - - -
226G ASN 2.9 35.4 + - - +
228G MET* 3.5 36.3 - - + -
231G LYS* 3.4 21.3 - - + +
270G CYS* 4.7 6.5 - - + -
271G HIS 3.5 2.7 - - - -
272G MET* 3.5 36.1 - - + -
297G TYR* 4.8 0.4 - - - -
371G PHE* 3.3 60.1 - + + -
374G LEU* 4.1 8.5 - - + -
375G LEU* 4.6 3.6 - - + -
1477G ADP 4.4 0.2 - - - -
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Residues in contact with GLY 127 (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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126G PHE* 1.3 76.2 - - - +
128G PRO* 1.3 66.3 - - - +
225G PHE* 3.9 3.6 - - - -
269G HIS 3.7 0.3 - - - +
270G CYS* 4.6 0.4 - - - -
271G HIS* 2.9 46.4 + - - -
1477G ADP 3.9 29.2 - - - +
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Residues in contact with PRO 128 (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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126G PHE* 5.1 0.4 - - + -
127G GLY* 1.3 88.9 - - - +
129G GLU* 1.3 60.6 + - - +
130G PRO* 3.2 8.6 - - - +
222G ALA* 5.9 0.2 - - - -
223G THR* 4.7 9.9 + - - +
231G LYS* 3.3 28.9 - - + -
235G ILE* 3.9 16.3 - - + +
268G MET* 3.8 26.9 - - + -
269G HIS 3.1 8.7 - - - +
270G CYS* 4.4 5.2 - - - -
371G PHE* 3.4 29.6 - - + -
1477G ADP 4.4 6.1 + - - +
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Residues in contact with GLU 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G PRO* 1.3 76.1 - - - +
130G PRO* 1.3 61.9 - - - +
131G GLU* 3.5 4.9 + - - +
220G GLU* 3.6 10.2 - - - +
221G VAL 5.9 0.7 - - - -
222G ALA* 5.9 4.0 - - + +
267G GLY 3.2 14.4 - - - +
268G MET* 3.4 6.3 - - - -
269G HIS* 2.7 29.2 + - + +
271G HIS* 3.1 16.5 + - + -
357G GLU* 2.5 10.6 - - - +
470G MN 2.0 38.4 + - - -
1477G ADP 2.6 59.9 + - - +
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Residues in contact with PRO 130 (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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128G PRO* 3.2 18.2 - - + +
129G GLU* 1.3 84.2 - - - +
131G GLU* 1.3 61.7 + - - +
132G PHE* 4.3 0.2 - - - -
220G GLU* 3.7 8.3 - - - +
221G VAL 4.9 3.8 - - - +
222G ALA* 6.2 0.2 - - - -
223G THR* 5.4 2.9 - - - +
235G ILE* 3.8 18.2 - - + -
238G TYR* 2.9 58.6 + - + -
239G LYS* 6.5 0.4 - - + -
255G PHE* 4.8 3.4 - - + -
267G GLY 3.7 4.7 - - - +
268G MET* 3.8 21.5 - - + -
363G PRO* 4.4 10.3 - - + -
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Residues in contact with GLU 131 (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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129G GLU 4.2 2.7 - - - +
130G PRO* 1.3 73.4 - - - +
132G PHE* 1.3 66.2 + - - +
212G GLU* 2.9 18.2 - - + +
218G GLN* 4.5 3.8 - - - +
219G ASN 3.8 5.8 - - - +
220G GLU* 3.3 22.2 - - + +
255G PHE* 3.5 6.3 - - - -
266G SER* 3.5 15.9 - - - +
267G GLY* 2.9 28.5 + - - +
269G HIS* 5.7 3.3 + - - -
363G PRO* 3.4 18.8 - - - +
469G MN 2.0 34.9 + - - -
474G TL 2.7 31.6 - - - -
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Residues in contact with PHE 132 (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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130G PRO 4.3 0.4 - - - -
131G GLU* 1.3 79.7 - - - +
133G PHE* 1.3 64.5 + - - +
134G LEU* 3.9 25.8 - - + -
192G ARG* 5.4 1.3 - - + -
195G MET* 3.8 23.3 - - + -
218G GLN* 3.2 7.6 - - - +
219G ASN* 2.8 64.0 + - + -
220G GLU* 4.0 6.3 - - - -
221G VAL* 4.2 7.9 - - + -
238G TYR* 3.6 24.0 - - - -
242G VAL* 3.8 26.9 - - + -
253G ALA* 4.7 0.2 - - + -
254G THR 3.4 15.7 - - - +
255G PHE* 3.6 22.4 - + + -
266G SER* 3.8 4.5 + - - -
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Residues in contact with PHE 133 (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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132G PHE* 1.3 75.1 - - - +
134G LEU* 1.3 61.9 + - - +
135G PHE* 3.7 23.3 - + + -
214G ALA* 3.5 15.0 - - + -
215G THR 3.7 3.8 - - - -
216G ALA 3.7 11.2 - - - -
217G GLY 3.3 2.9 - - - -
218G GLN* 3.5 32.1 - - + -
252G THR 3.8 0.9 - - - +
253G ALA* 3.2 8.7 - - - +
254G THR* 3.0 38.1 + - + +
256G MET 4.8 2.7 - - - -
259G PRO* 3.5 28.3 - - + -
260G MET* 3.4 24.5 - - + -
264G ASN 3.5 21.3 - - - -
266G SER* 3.4 26.5 - - - -
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Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G PHE* 3.9 19.5 - - + -
133G PHE* 1.3 73.4 - - - +
135G PHE* 1.3 62.2 + - - +
153G ASP* 3.4 12.7 - - - +
188G ALA* 4.6 10.3 - - + -
191G ILE* 4.0 30.3 - - + -
192G ARG* 5.7 1.6 - - + -
195G MET* 4.1 8.5 - - + -
216G ALA 3.5 13.3 - - - +
217G GLY* 2.8 16.9 + - - +
219G ASN* 3.9 17.9 - - - +
246G ALA* 3.8 17.5 - - + -
251G LYS* 4.0 15.8 + - + -
252G THR 3.6 2.0 - - - +
253G ALA* 3.6 28.0 - - + -
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Residues in contact with PHE 135 (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* 5.8 0.2 - + - -
466A TYR* 3.7 24.0 - + - -
133G PHE* 3.7 26.2 - + + -
134G LEU* 1.3 73.2 - - - +
136G ASP* 1.3 61.3 + - - +
137G ASP 4.2 5.2 - - - +
138G ILE* 4.8 4.3 - - + -
151G ILE* 3.6 40.4 - - + -
152G ASP 3.6 6.7 - - - +
153G ASP* 3.4 14.1 - - + -
216G ALA* 3.1 32.1 - - + -
251G LYS* 3.3 9.6 - - - +
252G THR* 2.9 40.8 + - + -
254G THR* 3.9 21.3 - - + -
259G PRO* 4.2 15.5 - - + -
260G MET* 4.6 2.9 - - + -
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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