Contacts of the helix formed by residues 308 - 319 (chain 0) in PDB entry 1O1F
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 308 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2190 VAL* 3.0 19.6 - - - +
2210 LEU* 4.7 5.6 - - - +
3060 TYR 3.5 0.2 + - - -
3070 PRO* 1.3 72.9 - - - +
3090 ILE* 1.3 62.7 + - - +
3100 ALA* 3.3 3.1 - - - +
3110 ASP* 4.0 22.1 - - - +
3120 ARG* 3.3 21.7 + - - +
3350 ARG* 5.9 0.2 - - - +
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Residues in contact with ILE 309 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1530 LEU* 5.7 4.7 - - + -
2190 VAL* 3.9 15.3 - - + -
2610 LEU* 4.3 13.5 - - + -
2620 PHE* 4.6 9.0 - - + -
2740 ILE* 6.2 2.5 - - + -
2990 MET* 4.3 13.7 - - + -
3030 THR 3.9 7.4 - - - +
3040 THR* 3.2 51.6 - - + +
3060 TYR* 3.2 25.8 - - + +
3070 PRO 3.2 1.0 - - - -
3080 GLY* 1.3 78.2 - - - +
3100 ALA* 1.3 71.8 + - + +
3120 ARG* 3.8 2.4 + - - +
3130 MET* 3.0 32.7 + - + +
3350 ARG* 3.5 14.1 - - - +
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Residues in contact with ALA 310 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2990 MET* 4.0 22.9 - - + -
3080 GLY* 5.7 0.9 - - - +
3090 ILE* 1.3 82.4 - - + +
3110 ASP* 1.4 53.6 + - - +
3130 MET* 3.1 3.1 + - - +
3140 GLN* 2.8 39.3 + - + +
3290 ILE* 4.1 14.8 - - + +
3310 ALA* 4.1 13.9 - - + -
3350 ARG* 5.5 0.4 - - - +
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Residues in contact with ASP 311 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2210 LEU* 3.8 32.4 - - + +
3080 GLY* 3.8 17.4 + - - +
3090 ILE 3.5 0.2 - - - -
3100 ALA* 1.4 73.6 - - - +
3120 ARG* 1.3 66.0 + - - +
3140 GLN* 3.1 11.0 - - - +
3150 LYS* 3.0 26.5 + - - +
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Residues in contact with ARG 312 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2190 VAL* 3.6 13.2 - - + -
2200 ALA 3.0 20.7 + - - +
2210 LEU* 3.8 15.2 - - - +
2220 ASP 4.9 2.9 - - - +
2230 PHE* 2.9 41.2 - - - +
2620 PHE* 3.3 25.8 - - + +
2630 GLN* 3.4 26.9 + - - +
3080 GLY 3.3 13.7 + - - +
3090 ILE 3.9 3.1 - - - +
3110 ASP* 1.3 78.2 - - - +
3130 MET* 1.3 52.1 + - - +
3150 LYS* 3.3 4.1 + - - +
3160 GLU* 2.7 76.6 + - - +
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Residues in contact with MET 313 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1530 LEU* 4.5 9.4 - - + -
2620 PHE* 4.2 10.3 - - + -
2740 ILE* 3.9 17.7 - - + -
2750 HIS* 3.4 34.8 - - - -
2780 THR* 3.0 36.1 - - + +
2970 ASN* 4.4 11.2 - - - +
2990 MET* 4.8 8.1 - - - -
3090 ILE* 3.0 24.6 + - + +
3100 ALA* 3.1 4.5 + - - +
3120 ARG* 1.3 71.5 - - - +
3140 GLN* 1.3 59.4 + - - +
3160 GLU* 3.6 2.3 - - - +
3170 ILE* 2.9 39.9 + - + +
3290 ILE* 4.1 16.6 - - + -
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Residues in contact with GLN 314 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3100 ALA* 2.8 13.4 + - + +
3110 ASP* 3.1 16.8 - - - +
3130 MET* 1.3 75.6 - - - +
3150 LYS* 1.3 63.5 + - + +
3180 THR* 2.8 34.8 + - - +
3270 ILE* 3.5 32.0 + - - +
3280 LYS* 4.3 2.0 - - - +
3290 ILE* 3.5 30.1 + - + +
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Residues in contact with LYS 315 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2210 LEU* 6.3 4.3 - - + -
3110 ASP 3.0 12.5 + - - +
3120 ARG* 4.0 4.0 - - - +
3140 GLN* 1.3 82.8 - - + +
3160 GLU* 1.3 66.5 + - - +
3180 THR* 3.1 34.3 + - + +
3190 ALA* 3.5 29.7 - - - +
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Residues in contact with GLU 316 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2620 PHE* 4.6 2.7 - - + -
2750 HIS* 3.2 57.8 + - + -
3120 ARG* 2.7 59.1 + - - +
3130 MET* 3.2 8.2 + - - +
3150 LYS* 1.3 81.4 - - - +
3170 ILE* 1.3 62.3 + - - +
3190 ALA* 3.9 3.5 + - - +
3200 LEU* 3.8 17.3 + - - +
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Residues in contact with ILE 317 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2750 HIS* 3.8 22.9 - - + +
2780 THR* 4.1 16.2 - - + -
2790 TYR* 5.1 6.2 - - + +
2940 TYR* 4.0 24.0 - - + +
2970 ASN* 3.9 13.7 - - - +
3130 MET* 2.9 28.4 + - + +
3160 GLU* 1.3 76.5 - - - +
3180 THR* 1.3 66.3 + - - +
3190 ALA 3.2 2.2 - - - -
3200 LEU* 3.0 6.5 + - + +
3210 ALA* 2.9 25.8 + - - +
3270 ILE* 3.7 26.5 - - + -
3290 ILE* 3.6 22.2 - - + -
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Residues in contact with THR 318 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3140 GLN* 2.8 30.2 + - - +
3150 LYS* 3.1 30.6 + - + +
3170 ILE* 1.3 73.5 - - - +
3190 ALA* 1.3 61.1 + - - +
3200 LEU 3.1 5.4 + - - -
3210 ALA* 3.1 20.8 - - - +
3230 SER* 5.8 0.7 - - - -
3250 MET 6.1 0.4 - - - +
3270 ILE* 3.7 29.2 - - + -
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Residues in contact with ALA 319 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3150 LYS* 3.5 29.5 + - - +
3160 GLU* 4.0 4.5 - - - +
3170 ILE 3.2 0.6 - - - -
3180 THR* 1.3 79.3 + - - +
3200 LEU* 1.3 58.9 + - - +
3210 ALA 4.8 0.9 - - - -
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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