Contacts of the helix formed by residues 308 - 319 (chain 2) 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 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2192 VAL* 3.0 19.2 - - - +
2212 LEU* 4.7 5.4 - - - +
3072 PRO* 1.3 72.2 - - - +
3092 ILE* 1.3 63.1 + - - +
3102 ALA* 3.3 4.2 - - - +
3112 ASP* 4.0 21.4 - - - +
3122 ARG* 3.3 21.1 + - - +
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Residues in contact with ILE 309 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1532 LEU* 5.7 4.3 - - + -
2192 VAL* 3.9 15.7 - - + -
2612 LEU* 4.3 14.1 - - + -
2622 PHE* 4.6 8.1 - - + -
2742 ILE* 6.2 2.7 - - + -
2992 MET* 4.3 14.4 - - + -
3032 THR 3.9 7.0 - - - +
3042 THR* 3.2 50.9 - - + +
3062 TYR* 3.2 26.5 - - + +
3072 PRO 3.2 1.0 - - - -
3082 GLY* 1.3 77.6 - - - +
3102 ALA* 1.3 74.8 + - + +
3122 ARG* 3.8 2.6 + - - +
3132 MET* 3.0 33.2 + - + +
3352 ARG* 3.5 13.7 - - - +
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Residues in contact with ALA 310 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2992 MET* 4.0 22.9 - - + -
3082 GLY* 5.2 1.3 - - - +
3092 ILE* 1.3 81.3 - - + +
3112 ASP* 1.4 54.4 + - - +
3132 MET* 3.1 4.0 + - - +
3142 GLN* 2.8 38.5 + - + +
3292 ILE* 4.1 15.3 - - + +
3312 ALA* 4.1 13.7 - - + -
3352 ARG* 5.5 0.4 - - - +
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Residues in contact with ASP 311 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2212 LEU* 3.8 32.4 - - + +
3082 GLY* 3.8 16.3 + - - +
3102 ALA* 1.4 72.8 - - - +
3122 ARG* 1.3 65.5 + - - +
3142 GLN* 3.2 11.3 - - - +
3152 LYS* 3.0 27.2 + - - +
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Residues in contact with ARG 312 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2192 VAL* 3.6 12.8 - - + -
2202 ALA 3.0 24.0 + - - +
2212 LEU* 3.8 11.7 - - - +
2222 ASP 4.9 2.7 - - - +
2232 PHE* 2.9 40.8 - - - +
2622 PHE* 3.3 26.2 - - + +
2632 GLN* 3.4 26.7 + - - +
3082 GLY 3.3 15.4 + - - +
3092 ILE 3.9 2.9 - - - +
3112 ASP* 1.3 78.2 - - - +
3132 MET* 1.3 51.6 + - - +
3152 LYS* 3.3 4.1 + - - +
3162 GLU* 2.7 76.7 + - - +
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Residues in contact with MET 313 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1532 LEU* 4.5 8.7 - - + -
2622 PHE* 4.2 11.0 - - + -
2742 ILE* 3.9 17.7 - - + -
2752 HIS* 3.4 33.7 - - - -
2782 THR* 3.0 36.6 - - + +
2972 ASN* 4.4 11.0 - - - +
2992 MET* 4.8 10.1 - - - -
3092 ILE* 3.0 25.1 + - + +
3102 ALA* 3.1 4.9 + - - +
3122 ARG* 1.3 72.7 - - - +
3142 GLN* 1.3 59.2 + - - +
3162 GLU* 3.6 1.5 - - - +
3172 ILE* 2.9 39.5 + - + +
3292 ILE* 4.1 17.5 - - + -
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Residues in contact with GLN 314 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3102 ALA* 2.8 12.5 + - + +
3112 ASP* 3.2 16.8 - - - +
3132 MET* 1.3 76.1 - - - +
3152 LYS* 1.3 61.3 + - + +
3182 THR* 2.8 34.8 + - - +
3272 ILE* 3.5 32.3 + - - +
3282 LYS* 4.3 2.0 - - - +
3292 ILE* 3.5 31.0 + - + +
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Residues in contact with LYS 315 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2212 LEU* 6.3 4.0 - - + -
3112 ASP 3.0 11.9 + - - +
3122 ARG* 4.0 3.4 - - - +
3142 GLN* 1.3 82.7 - - + +
3162 GLU* 1.3 66.8 + - + +
3182 THR* 3.1 34.7 + - + +
3192 ALA* 3.5 30.3 - - - +
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Residues in contact with GLU 316 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2622 PHE* 4.6 2.5 - - + -
2752 HIS* 3.2 56.7 + - + -
3122 ARG* 2.7 60.5 + - - +
3132 MET* 3.2 8.3 + - - +
3152 LYS* 1.3 81.1 - - - +
3172 ILE* 1.3 61.6 + - - +
3192 ALA* 3.9 3.9 + - - +
3202 LEU* 3.8 16.8 + - - +
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Residues in contact with ILE 317 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2752 HIS* 3.8 22.4 - - + +
2782 THR* 4.1 15.7 - - + -
2792 TYR* 5.1 5.6 - - + +
2942 TYR* 4.0 25.6 - - + +
2972 ASN* 3.9 13.7 - - - +
3132 MET* 2.9 28.1 + - + +
3162 GLU* 1.3 77.4 - - - +
3182 THR* 1.3 66.7 + - - +
3192 ALA 3.2 1.8 - - - -
3202 LEU* 3.0 5.9 + - + +
3212 ALA* 2.9 25.1 + - - +
3272 ILE* 3.7 26.0 - - + -
3292 ILE* 3.6 21.1 - - + -
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Residues in contact with THR 318 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3142 GLN* 2.8 31.1 + - - +
3152 LYS* 3.1 31.0 + - + +
3172 ILE* 1.3 72.7 - - - +
3192 ALA* 1.3 60.9 + - - +
3202 LEU 3.1 5.7 + - - -
3212 ALA* 3.1 20.4 + - - +
3232 SER* 5.8 0.9 - - - -
3252 MET 6.1 0.4 - - - +
3272 ILE* 3.7 29.4 - - + -
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Residues in contact with ALA 319 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3152 LYS* 3.5 28.2 + - - +
3162 GLU 4.0 4.7 - - - +
3172 ILE 3.2 0.2 - - - -
3182 THR* 1.3 79.7 + - - +
3202 LEU* 1.3 59.1 + - - +
3212 ALA 4.8 0.4 - - - -
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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