Contacts of the helix formed by residues 3109 - 3119 (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 SER3109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3078C LYS* 3.9 1.1 - - - -
3107C VAL 3.8 0.2 + - - -
3108C MET* 1.3 76.5 - - - +
3110C ASP* 1.3 54.7 + - - +
3111C GLU* 3.7 11.3 - - - +
3112C VAL* 3.0 27.2 + - - +
3113C GLU* 2.7 32.2 + - - +
4100D GLU* 2.7 29.7 + - - +
4103D ARG* 4.7 7.4 - - - +
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Residues in contact with ASP3110 (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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3074C ALA* 6.0 0.2 - - - +
3078C LYS* 2.7 22.3 + - - +
3109C SER* 1.3 70.4 - - - +
3111C GLU* 1.3 67.2 + - - +
3113C GLU* 2.8 13.9 + - - +
3114C ARG* 2.8 50.1 + - - +
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Residues in contact with GLU3111 (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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3109C SER* 3.7 11.6 - - - +
3110C ASP* 1.3 80.7 - - - +
3112C VAL* 1.3 59.7 + - - +
3114C ARG* 3.5 24.5 + - - +
3115C ARG* 3.3 27.6 + - - +
4092D LEU* 3.1 20.5 - - + +
4093D ASP* 3.7 7.4 + - - +
4096D LYS* 2.9 49.7 + - + +
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Residues in contact with VAL3112 (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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3108C MET* 4.0 20.4 - - + -
3109C SER* 3.0 25.7 + - - +
3111C GLU* 1.3 74.0 - - - +
3113C GLU* 1.3 66.3 + - - +
3115C ARG* 3.8 6.7 - - - +
3116C LEU* 2.9 27.1 + - + +
4086D LEU* 4.2 4.7 - - + -
4090D ILE* 4.3 14.1 - - + -
4092D LEU* 3.7 33.4 - - + -
4100D GLU* 3.7 13.7 - - - +
4104D TRP* 4.1 16.2 - - + -
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Residues in contact with GLU3113 (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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3074C ALA* 4.8 1.9 - - - +
3077C ARG* 3.0 42.2 + - - +
3078C LYS* 2.8 33.2 + - + +
3081C LEU* 3.4 25.3 - - + +
3108C MET* 3.2 16.8 - - + +
3109C SER 2.7 16.8 + - - +
3110C ASP* 3.1 16.4 - - - +
3112C VAL* 1.3 74.1 - - - +
3114C ARG* 1.3 66.5 + - - +
3116C LEU* 3.2 3.6 + - - +
3117C VAL* 3.2 18.7 + - - +
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Residues in contact with ARG3114 (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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3110C ASP* 2.8 42.0 + - - +
3111C GLU* 3.5 31.8 + - - +
3113C GLU* 1.3 78.0 - - + +
3115C ARG* 1.3 65.9 - - - +
3117C VAL* 2.8 31.8 - - + +
3118C LYS* 3.3 7.4 + - - +
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Residues in contact with ARG3115 (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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3111C GLU* 3.3 28.4 + - - +
3112C VAL* 3.4 6.0 + - - +
3114C ARG* 1.3 77.8 - - - +
3116C LEU* 1.3 57.9 + - - +
3118C LYS* 3.4 26.3 + - - +
3119C VAL* 3.0 56.2 + - - +
4090D ILE* 3.2 28.7 + - + -
4091D GLY* 3.0 34.1 + - - -
4092D LEU* 4.1 9.4 - - + +
4093D ASP 5.3 0.7 - - - +
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Residues in contact with LEU3116 (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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3081C LEU* 4.0 28.9 - - + +
3082C ALA* 5.1 0.7 - - - -
3085C LEU* 4.1 16.6 - - + -
3108C MET* 3.7 27.1 - - + -
3112C VAL* 2.9 18.5 + - + +
3113C GLU 3.4 5.8 - - - +
3114C ARG 3.0 0.2 - - - -
3115C ARG* 1.3 74.2 - - - +
3117C VAL* 1.3 63.3 + - - +
3118C LYS 3.1 2.2 + - - -
3119C VAL* 3.6 8.9 + - + +
3120C LEU* 3.0 42.0 + - + +
4090D ILE* 3.1 44.9 - - + -
4104D TRP* 5.9 3.1 - - + -
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Residues in contact with VAL3117 (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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3081C LEU* 4.1 17.0 - - + +
3084C ARG* 5.8 5.7 + - - +
3113C GLU 3.2 8.0 + - - +
3114C ARG* 2.8 32.0 + - + +
3116C LEU* 1.3 76.8 - - - +
3118C LYS* 1.3 67.9 + - + +
3120C LEU* 3.9 8.1 + - - +
3121C LYS 4.1 9.9 - - - +
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Residues in contact with LYS3118 (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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3114C ARG 3.3 7.8 + - - +
3115C ARG* 3.6 29.2 - - - +
3116C LEU 3.1 0.2 - - - -
3117C VAL* 1.3 83.8 - - + +
3119C VAL* 1.3 52.2 + - - +
3120C LEU 2.8 16.3 + - - -
3121C LYS* 3.5 13.4 + - - +
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Residues in contact with VAL3119 (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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3089C ILE* 5.3 1.4 - - - +
3115C ARG* 3.0 46.0 + - - +
3116C LEU* 3.6 29.2 - - + +
3118C LYS* 1.3 71.0 - - + +
3120C LEU* 1.3 66.5 + - + +
3121C LYS* 3.6 2.1 - - - +
4089D ILE* 4.3 12.6 - - + +
4090D ILE* 3.6 23.8 - - + +
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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