Contacts of the helix formed by residues 3026 - 3035 (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 LEU3026 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3018C LEU* 5.1 0.2 - - - +
3024C THR* 2.9 25.1 + - + +
3025C PRO* 1.3 74.2 - - - +
3027C ARG* 1.3 60.1 + - - +
3028C ALA* 4.1 6.7 - - + +
3029C ARG* 2.8 37.6 + - + +
3030C ILE* 3.5 5.5 + - - +
3059C ASP 4.4 3.8 - - - +
3060C ARG* 3.5 30.1 - - + +
3061C SER* 4.2 3.8 - - - +
3062C LEU* 4.5 3.1 - - - -
413F G 3.9 35.2 - - - +
414F G 3.4 19.5 - - - +
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Residues in contact with ARG3027 (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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3026C LEU* 1.3 71.7 - - - +
3028C ALA* 1.3 64.7 + - - +
3030C ILE* 2.9 16.6 + - - +
3031C ALA* 3.1 9.9 + - - +
3038C GLY 6.1 0.2 - - - +
3041C VAL* 3.6 17.4 - - + +
3042C SER* 4.0 31.5 + - - +
3045C VAL* 4.3 16.0 - - + +
3056C VAL* 3.9 28.2 - - - +
3060C ARG* 4.3 14.4 + - - +
3062C LEU* 4.0 25.5 - - + +
414F G 2.9 44.6 + - - +
415F T 3.1 27.0 + - - -
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Residues in contact with ALA3028 (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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3026C LEU* 3.1 3.1 - - + -
3027C ARG* 1.3 71.9 - - - +
3029C ARG* 1.3 81.1 + - - +
3031C ALA* 3.2 11.0 - - - +
3032C GLU* 3.1 22.5 + - + +
413F G 4.0 25.4 - - + +
414F G 2.7 24.5 + - - +
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Residues in contact with ARG3029 (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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3018C LEU* 3.4 26.0 - - + -
3023C VAL* 4.1 17.0 - - + +
3024C THR 3.8 20.9 - - - +
3026C LEU* 2.8 24.0 + - + +
3028C ALA* 1.3 88.1 - - - +
3030C ILE* 1.3 64.0 + - - +
3032C GLU* 2.7 39.4 + - - +
3033C ARG* 3.0 32.3 + - + +
413F G 2.6 42.4 + - - -
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Residues in contact with ILE3030 (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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3011C TYR* 3.8 38.1 - - + +
3014C THR* 4.3 21.1 - - + -
3015C ILE* 4.1 13.0 - - + -
3018C LEU* 5.2 2.0 - - + -
3025C PRO 6.3 0.2 - - - -
3026C LEU 3.5 6.0 + - - +
3027C ARG* 2.9 8.7 + - - +
3029C ARG* 1.3 74.0 - - + +
3031C ALA* 1.3 60.8 + - - +
3033C ARG 3.2 0.9 + - - -
3034C LEU* 2.7 60.0 + - + +
3041C VAL* 4.0 9.0 - - + -
3045C VAL* 4.4 5.2 - - + -
3062C LEU* 3.4 31.0 - - + -
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Residues in contact with ALA3031 (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 3.1 8.6 + - - +
3028C ALA* 3.2 14.1 - - - +
3030C ILE* 1.3 79.0 - - - +
3032C GLU* 1.3 54.0 + - + +
3035C GLU* 2.8 36.0 + - - -
3036C GLN 3.2 20.9 + - - +
3038C GLY* 5.0 9.4 - - - -
3041C VAL* 3.8 18.3 - - + +
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Residues in contact with GLU3032 (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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3028C ALA* 3.1 11.9 + - + +
3029C ARG* 2.7 51.1 + - - +
3030C ILE 3.3 0.2 - - - -
3031C ALA* 1.3 81.8 - - - +
3033C ARG* 1.3 66.7 + - + +
3035C GLU* 3.3 14.7 + - - +
413F G 4.4 3.3 + - - -
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Residues in contact with ARG3033 (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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3014C THR* 3.7 26.7 + - + +
3017C GLU* 4.3 20.2 + - - +
3018C LEU* 3.2 27.4 - - - +
3021C GLU* 2.6 42.2 + - - -
3023C VAL* 5.1 1.6 - - - +
3029C ARG* 3.0 20.0 + - - +
3030C ILE 3.8 1.6 - - - +
3032C GLU* 1.3 83.1 + - + +
3034C LEU* 1.3 65.3 + - + +
3035C GLU* 3.1 9.6 + - - +
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Residues in contact with LEU3034 (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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3004C LEU* 4.1 30.1 - - + +
3010C MET* 4.2 19.7 - - + +
3011C TYR* 3.3 41.1 - - + -
3014C THR* 3.4 24.7 - - - +
3030C ILE* 2.7 28.6 + - + +
3033C ARG* 1.3 77.1 - - + +
3035C GLU* 1.3 73.8 + - - +
3036C GLN* 3.4 18.0 + - + +
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Residues in contact with GLU3035 (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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3031C ALA 2.8 12.9 + - - -
3032C GLU* 3.7 12.6 - - - +
3033C ARG 3.1 6.9 - - - +
3034C LEU* 1.3 83.7 - - - +
3036C GLN* 1.3 58.7 + - - +
317E C 4.2 5.9 + - - -
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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