Contacts of the helix formed by residues 308 - 319 (chain 1) 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 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2191 VAL* 3.0 19.9 - - - +
2211 LEU* 4.7 5.4 - - - +
3071 PRO* 1.3 72.0 - - - +
3091 ILE* 1.3 63.8 + - - +
3101 ALA* 3.3 3.3 - - - +
3111 ASP* 4.0 22.1 - - - +
3121 ARG* 3.3 21.3 + - - +
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Residues in contact with ILE 309 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1531 LEU* 5.7 4.5 - - + -
2191 VAL* 3.9 15.3 - - + -
2611 LEU* 4.3 14.4 - - + -
2621 PHE* 4.6 8.8 - - + -
2741 ILE* 6.2 2.7 - - + -
2991 MET* 4.3 13.5 - - + -
3031 THR 3.9 7.0 - - - +
3041 THR* 3.2 52.3 - - + +
3061 TYR* 3.2 25.4 - - + +
3071 PRO 3.2 1.6 - - - -
3081 GLY* 1.3 77.7 - - - +
3101 ALA* 1.3 72.8 - - + +
3121 ARG* 3.8 2.3 + - - +
3131 MET* 3.0 33.3 + - + +
3351 ARG* 3.5 14.1 - - - +
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Residues in contact with ALA 310 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2991 MET* 4.0 22.7 - - + -
3081 GLY* 5.7 0.7 - - - -
3091 ILE* 1.3 82.6 - - + +
3111 ASP* 1.4 54.3 + - - +
3131 MET* 3.1 3.6 + - - +
3141 GLN* 2.8 38.8 + - + +
3291 ILE* 4.1 15.0 - - + +
3311 ALA* 4.1 14.1 - - + -
3351 ARG* 5.5 0.7 - - - +
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Residues in contact with ASP 311 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2211 LEU* 3.8 32.1 - - + +
3081 GLY* 3.8 16.3 + - - +
3091 ILE 3.5 0.2 - - - -
3101 ALA* 1.4 72.6 - - - +
3121 ARG* 1.3 65.3 + - - +
3141 GLN* 3.1 10.8 - - - +
3151 LYS* 3.0 27.0 + - - +
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Residues in contact with ARG 312 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2191 VAL* 3.6 12.8 - - + -
2201 ALA 3.0 24.7 + - - +
2211 LEU* 3.8 11.0 - - - +
2221 ASP 4.9 2.7 - - - +
2231 PHE* 2.9 41.3 - - - +
2621 PHE* 3.3 25.5 - - + +
2631 GLN* 3.4 27.3 + - - +
3081 GLY 3.3 14.8 + - - +
3091 ILE 3.9 3.4 - - - +
3101 ALA 3.4 0.2 - - - -
3111 ASP* 1.3 77.0 - - - +
3131 MET* 1.3 51.7 + - - +
3151 LYS* 3.3 4.1 + - - +
3161 GLU* 2.7 77.4 + - - +
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Residues in contact with MET 313 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1531 LEU* 4.5 9.0 - - + -
2621 PHE* 4.2 11.2 - - + -
2741 ILE* 3.9 17.5 - - + -
2751 HIS* 3.4 34.1 - - - -
2781 THR* 3.0 36.1 - - + +
2971 ASN* 4.4 11.2 - - - +
2991 MET* 4.8 9.0 - - - -
3091 ILE* 3.0 24.4 + - + +
3101 ALA* 3.1 4.7 + - - +
3121 ARG* 1.3 71.7 - - - +
3141 GLN* 1.3 60.0 + - - +
3161 GLU* 3.6 2.3 - - - +
3171 ILE* 2.9 39.3 + - + +
3291 ILE* 4.1 16.8 - - + -
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Residues in contact with GLN 314 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3101 ALA* 2.8 13.4 + - + +
3111 ASP* 3.1 17.5 - - - +
3131 MET* 1.3 76.5 - - - +
3151 LYS* 1.3 60.9 + - + +
3181 THR* 2.8 35.5 + - - +
3271 ILE* 3.5 32.6 + - - +
3281 LYS* 4.3 2.2 - - - +
3291 ILE* 3.5 29.9 + - + +
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Residues in contact with LYS 315 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2211 LEU* 6.3 4.0 - - + -
3111 ASP 3.0 12.4 + - - +
3121 ARG* 4.0 3.8 - - - +
3141 GLN* 1.3 83.4 - - + +
3161 GLU* 1.3 65.6 + - - +
3181 THR* 3.1 35.0 + - + +
3191 ALA* 3.5 30.0 - - - +
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Residues in contact with GLU 316 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2621 PHE* 4.6 2.2 - - + -
2751 HIS* 3.2 56.5 + - + +
3121 ARG* 2.7 59.8 + - - +
3131 MET* 3.2 8.0 + - - +
3151 LYS* 1.3 80.3 - - + +
3171 ILE* 1.3 61.4 + - - +
3191 ALA* 3.9 3.5 + - - +
3201 LEU* 3.8 17.0 + - - +
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Residues in contact with ILE 317 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2751 HIS* 3.8 22.9 - - + +
2781 THR* 4.1 16.2 - - + -
2791 TYR* 5.1 6.1 - - + +
2941 TYR* 4.0 25.1 - - + +
2971 ASN* 3.9 13.9 - - - +
3131 MET* 2.9 27.5 + - + +
3161 GLU* 1.3 76.3 - - - +
3181 THR* 1.3 67.2 + - - +
3191 ALA 3.2 1.8 - - - -
3201 LEU* 3.0 5.3 + - + +
3211 ALA* 2.9 25.6 + - - +
3271 ILE* 3.7 26.5 - - + -
3291 ILE* 3.6 21.8 - - + -
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Residues in contact with THR 318 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3141 GLN* 2.8 30.1 + - - +
3151 LYS* 3.1 30.3 + - + +
3171 ILE* 1.3 73.8 - - - +
3191 ALA* 1.3 60.7 + - - +
3201 LEU 3.1 5.7 + - - -
3211 ALA* 3.1 21.0 + - - +
3231 SER* 5.8 0.7 - - - -
3251 MET 6.1 0.7 - - - +
3271 ILE* 3.7 29.8 - - + -
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Residues in contact with ALA 319 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3151 LYS* 3.5 27.3 + - - +
3161 GLU 4.0 4.7 - - - +
3171 ILE 3.2 0.4 - - - -
3181 THR* 1.3 80.5 + - - +
3201 LEU* 1.3 57.6 + - - +
3211 ALA 4.8 0.7 - - - -
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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