Contacts of the helix formed by residues 308 - 319 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2194 VAL* 3.0 20.4 - - - +
2214 LEU* 4.7 5.6 - - - +
3064 TYR 3.5 0.2 + - - -
3074 PRO* 1.3 72.2 - - - +
3094 ILE* 1.3 63.2 + - - +
3104 ALA* 3.3 3.5 - - - +
3114 ASP* 4.0 22.4 - - - +
3124 ARG* 3.3 21.5 + - - +
3354 ARG* 5.9 0.2 - - - +
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Residues in contact with ILE 309 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1534 LEU* 5.7 4.7 - - + -
2194 VAL* 3.9 15.0 - - + -
2614 LEU* 4.3 13.5 - - + -
2624 PHE* 4.6 8.8 - - + -
2744 ILE* 6.2 2.7 - - + -
2994 MET* 4.3 13.5 - - + -
3034 THR 3.9 7.2 - - - +
3044 THR* 3.2 52.3 - - + +
3064 TYR* 3.2 25.8 - - + +
3074 PRO 3.2 1.4 - - - -
3084 GLY* 1.3 78.0 - - - +
3104 ALA* 1.3 72.5 + - + +
3124 ARG* 3.8 2.4 + - - +
3134 MET* 3.0 33.0 + - + +
3354 ARG* 3.5 13.7 - - - +
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Residues in contact with ALA 310 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2994 MET* 4.0 22.7 - - + -
3084 GLY* 5.7 0.9 - - - +
3094 ILE* 1.3 82.0 - - + +
3114 ASP* 1.4 53.6 + - - +
3134 MET* 3.1 3.5 + - - +
3144 GLN* 2.8 38.8 + - + +
3294 ILE* 4.1 15.0 - - + +
3314 ALA* 4.1 14.1 - - + -
3354 ARG* 5.5 0.4 - - - +
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Residues in contact with ASP 311 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2214 LEU* 3.8 31.6 - - + +
3084 GLY* 3.8 17.1 + - - +
3094 ILE 3.5 0.2 - - - -
3104 ALA* 1.4 72.9 - - - +
3124 ARG* 1.3 66.2 + - - +
3144 GLN* 3.1 11.1 - - - +
3154 LYS* 3.0 26.3 + - - +
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Residues in contact with ARG 312 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2194 VAL* 3.6 12.1 - - + -
2204 ALA 3.0 21.1 + - - +
2214 LEU* 3.8 15.2 - - - +
2224 ASP 4.9 3.1 - - - +
2234 PHE* 2.9 41.6 - - - +
2624 PHE* 3.3 26.1 - - + +
2634 GLN* 3.4 27.3 + - - +
3084 GLY 3.3 14.0 + - - +
3094 ILE 3.9 2.9 - - - +
3114 ASP* 1.3 78.0 - - - +
3134 MET* 1.3 52.2 + - - +
3154 LYS* 3.3 3.9 + - - +
3164 GLU* 2.7 76.2 + - - +
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Residues in contact with MET 313 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1534 LEU* 4.5 9.4 - - + -
2624 PHE* 4.2 10.3 - - + -
2744 ILE* 3.9 17.7 - - + -
2754 HIS* 3.4 34.3 - - - -
2784 THR* 3.0 36.1 - - + +
2974 ASN* 4.4 11.2 - - - +
2994 MET* 4.8 8.1 - - - -
3094 ILE* 3.0 24.6 + - + +
3104 ALA* 3.1 4.2 + - - +
3124 ARG* 1.3 71.8 - - - +
3144 GLN* 1.3 58.7 + - - +
3164 GLU* 3.6 1.6 - - - +
3174 ILE* 2.9 39.1 + - + +
3294 ILE* 4.1 17.5 - - + -
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Residues in contact with GLN 314 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3104 ALA* 2.8 13.5 + - + +
3114 ASP* 3.1 17.0 - - - +
3134 MET* 1.3 75.3 - - - +
3154 LYS* 1.3 62.6 + - + +
3184 THR* 2.8 34.7 + - - +
3274 ILE* 3.5 32.4 + - - +
3284 LYS* 4.3 2.2 - - - +
3294 ILE* 3.5 30.1 + - + +
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Residues in contact with LYS 315 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2214 LEU* 6.3 4.0 - - + -
3114 ASP 3.0 12.8 + - - +
3124 ARG* 4.0 3.8 - - - +
3144 GLN* 1.3 83.4 - - + +
3164 GLU* 1.3 67.1 + - - +
3184 THR* 3.1 33.2 + - + +
3194 ALA* 3.5 29.7 - - - +
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Residues in contact with GLU 316 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2624 PHE* 4.6 3.1 - - + -
2754 HIS* 3.2 57.8 + - + -
3124 ARG* 2.7 60.1 + - - +
3134 MET* 3.2 7.8 + - - +
3154 LYS* 1.3 82.0 - - - +
3174 ILE* 1.3 61.6 + - - +
3194 ALA* 3.9 3.7 + - - +
3204 LEU* 3.8 17.2 + - - +
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Residues in contact with ILE 317 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2754 HIS* 3.8 23.1 - - + +
2784 THR* 4.1 16.4 - - + -
2794 TYR* 5.1 5.6 - - + +
2944 TYR* 4.0 24.9 - - + +
2974 ASN* 3.9 13.9 - - - +
3134 MET* 2.9 27.7 + - + +
3164 GLU* 1.3 76.1 - - - +
3184 THR* 1.3 66.3 + - - +
3194 ALA 3.2 2.5 - - - -
3204 LEU* 3.0 6.1 + - + +
3214 ALA* 2.9 25.6 + - - +
3274 ILE* 3.7 26.5 - - + -
3294 ILE* 3.6 22.0 - - + -
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Residues in contact with THR 318 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3144 GLN* 2.8 30.8 + - - +
3154 LYS* 3.1 30.8 + - + +
3174 ILE* 1.3 73.4 - - - +
3194 ALA* 1.3 61.7 + - - +
3204 LEU 3.1 5.5 + - - -
3214 ALA* 3.1 20.8 - - - +
3234 SER* 5.8 0.7 - - - -
3254 MET 6.1 0.4 - - - +
3274 ILE* 3.7 29.8 - - + -
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Residues in contact with ALA 319 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3154 LYS* 3.5 28.9 + - - +
3164 GLU* 4.0 4.3 - - - +
3174 ILE 3.2 0.8 - - - -
3184 THR* 1.3 80.1 + - - +
3204 LEU* 1.3 58.7 + - - +
3214 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