Contacts of the helix formed by residues 3037 - 3051 (chain C) in PDB entry 1F5T
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 SER3037 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3036C GLN* 1.3 73.7 - - - +
3038C GLY* 1.3 65.1 + - - +
3039C PRO* 3.0 9.8 - - - +
3040C THR* 2.9 21.3 + - - -
3041C VAL* 3.1 12.2 + - - +
317E C 2.9 28.0 + - - -
318E T 3.0 43.2 - - - +
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Residues in contact with GLY3038 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3027C ARG* 6.1 0.2 - - - +
3031C ALA* 5.0 8.0 - - - +
3036C GLN 3.7 2.4 + - - -
3037C SER* 1.3 71.6 - - - +
3039C PRO* 1.3 68.1 - - - +
3041C VAL* 3.4 7.5 + - - +
3042C SER* 3.3 23.7 + - - -
415F T 4.4 9.6 - - - +
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Residues in contact with PRO3039 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3037C SER* 3.0 11.0 - - - +
3038C GLY* 1.3 88.9 - - - +
3040C THR* 1.3 61.9 + - - +
3042C SER* 3.9 7.6 - - - -
3043C GLN* 3.3 30.1 + - - +
317E C 4.6 4.9 - - - +
318E T 3.6 24.9 - - + +
319E A 4.0 4.3 - - - +
415F T 3.9 20.0 - - + +
416F T 3.4 30.7 - - + +
417F A 4.4 4.3 - - - +
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Residues in contact with THR3040 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3036C GLN* 3.8 18.4 - - - +
3037C SER* 2.9 16.8 + - - -
3039C PRO* 1.3 75.3 - - - +
3041C VAL* 1.3 65.7 + - - +
3043C GLN* 3.4 10.3 + - + +
3044C THR* 3.0 35.4 + - - +
315E G 4.8 1.6 - - + -
316E C 3.1 42.6 - - + +
317E C 2.6 30.8 + - - +
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Residues in contact with VAL3041 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3011C TYR* 3.3 23.6 - - + +
3027C ARG* 3.6 35.4 - - + +
3030C ILE* 4.0 13.9 - - + -
3031C ALA* 3.8 31.0 - - + +
3036C GLN* 4.3 9.0 - - + -
3037C SER 3.1 12.8 + - - +
3038C GLY* 3.7 7.4 - - - +
3040C THR* 1.3 77.4 - - - +
3042C SER* 1.3 56.7 + - - +
3044C THR* 3.9 0.9 - - - -
3045C VAL* 2.9 32.7 + - + +
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Residues in contact with SER3042 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3027C ARG* 4.0 22.8 + - - +
3038C GLY 3.3 14.8 + - - -
3039C PRO* 4.0 8.3 - - - -
3040C THR 3.3 0.2 - - - -
3041C VAL* 1.3 75.4 - - - +
3043C GLN* 1.3 65.7 + - - +
3045C VAL* 3.9 1.6 - - - +
3046C ALA* 3.0 24.4 + - - +
414F G 4.8 1.0 + - - -
415F T 2.7 32.2 + - - +
416F T 6.0 3.1 - - - -
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Residues in contact with GLN3043 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3039C PRO* 3.3 17.7 + - - +
3040C THR* 3.6 11.8 - - - +
3042C SER* 1.3 76.4 - - - +
3044C THR* 1.3 55.9 + - - +
3046C ALA* 2.8 10.3 + - - +
3047C ARG* 2.8 46.2 + - - +
315E G 4.2 8.5 - - - +
316E C 3.5 30.6 + - - +
317E C 3.1 29.9 - - - +
418F G 4.9 1.3 + - - -
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Residues in contact with THR3044 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3007C THR* 3.8 23.4 - - + +
3008C THR* 5.6 1.8 - - - +
3011C TYR* 3.5 38.1 + - + -
3036C GLN* 4.8 0.5 + - - -
3040C THR* 3.0 22.7 + - - +
3043C GLN* 1.3 80.2 - - - +
3045C VAL* 1.3 57.2 + - - +
3047C ARG* 3.2 29.1 + - - +
3048C MET* 2.8 38.6 + - + +
315E G 5.0 3.1 - - - +
316E C 4.9 1.9 + - - -
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Residues in contact with VAL3045 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3011C TYR* 4.1 18.6 - - + -
3015C ILE* 5.8 0.9 - - + -
3027C ARG* 4.3 9.6 - - - -
3030C ILE* 4.4 0.2 - - + -
3041C VAL* 2.9 32.5 + - + +
3042C SER 3.9 3.1 - - - +
3044C THR* 1.3 71.1 - - - +
3046C ALA* 1.3 53.5 + - - +
3048C MET* 2.7 14.5 + - - +
3049C GLU* 2.5 33.9 + - + +
3054C VAL* 4.1 15.7 - - + -
3056C VAL* 3.9 28.0 - - + -
3062C LEU* 4.3 26.2 - - + -
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Residues in contact with ALA3046 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3042C SER 3.0 14.2 + - - +
3043C GLN* 2.8 12.9 + - - +
3045C VAL* 1.3 77.8 - - - +
3047C ARG* 1.3 56.0 + - - +
3049C GLU* 3.0 15.4 + - - +
3050C ARG* 2.7 30.0 + - - +
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Residues in contact with ARG3047 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3043C GLN* 2.8 29.2 + - - +
3044C THR* 3.3 36.8 + - - +
3046C ALA* 1.3 70.7 - - - +
3048C MET* 1.3 63.2 + - + +
3050C ARG* 3.1 40.7 - - - +
3051C ASP* 3.0 20.2 + - - +
314E A 3.6 41.1 + - - +
315E G 3.3 52.2 + - - +
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Residues in contact with MET3048 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3008C THR* 4.4 25.8 - - + +
3011C TYR* 3.7 42.6 - - + -
3012C LEU* 3.9 32.1 - - + +
3015C ILE* 5.1 5.4 - - + -
3044C THR* 2.8 20.0 + - + +
3045C VAL* 2.7 16.4 + - - +
3047C ARG* 1.3 75.2 - - + +
3049C GLU* 1.3 62.7 + - - +
3051C ASP* 3.1 8.4 + - - +
3052C GLY 3.1 15.6 + - - -
3053C LEU* 3.1 22.7 + - + +
3054C VAL* 3.9 18.4 - - + -
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Residues in contact with GLU3049 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3045C VAL* 2.5 15.9 + - + +
3046C ALA* 3.4 15.5 - - - +
3048C MET* 1.3 72.1 - - - +
3050C ARG* 1.3 58.5 + - - +
3052C GLY* 2.9 19.1 + - - -
3054C VAL* 3.5 24.4 - - + +
3055C VAL* 3.5 12.4 - - + +
3056C VAL* 3.0 45.2 + - - +
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Residues in contact with ARG3050 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3046C ALA 2.7 12.8 + - - +
3047C ARG* 3.1 28.3 + - - +
3049C GLU* 1.3 78.3 - - - +
3051C ASP* 1.3 86.5 + - - +
3052C GLY 3.4 1.9 + - - -
313E T 4.9 0.8 + - - -
314E A 2.9 40.8 + - - -
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Residues in contact with ASP3051 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3047C ARG* 3.0 19.5 + - - +
3048C MET* 3.1 10.1 + - - +
3050C ARG* 1.3 109.9 + - - +
3052C GLY* 1.3 65.0 + - - +
3053C LEU* 3.6 14.5 + - + +
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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