Contacts of the helix formed by residues 5118 - 5131 (chain K) in PDB entry 1F2I
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 ARG5118 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5006E C 3.5 32.7 - - - +
5007E G 2.7 49.1 + - - -
6008F C 3.8 3.8 - - - +
5105K TYR* 3.5 4.5 - - - -
5116K PHE* 3.9 3.6 - - - +
5117K SER* 1.3 84.7 - - - +
5119K SER* 1.3 65.6 + - - +
5120K ASP* 2.7 35.8 + - - +
5121K GLU* 3.0 37.1 + - - +
5122K LEU 3.5 3.5 + - - -
6117L SER 5.2 0.7 - - - -
6118L ARG* 3.4 50.8 - - + +
6119L SER* 5.4 2.7 - - - +
6120L ASP* 4.8 5.1 + - - -
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Residues in contact with SER5119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5105K TYR* 3.2 43.3 - - - -
5118K ARG* 1.3 71.7 - - - +
5120K ASP* 1.3 63.9 + - - +
5122K LEU* 3.2 5.2 + - - +
5123K THR* 3.1 25.8 + - - -
6099L VAL* 3.9 19.9 + - - +
6100L PRO 5.8 0.2 - - - -
6101L LYS* 6.5 1.1 - - - -
6117L SER* 5.1 7.5 + - - -
6118L ARG* 5.8 0.8 - - - +
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Residues in contact with ASP5120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5006E C 4.0 9.9 + - - -
6006F C 6.2 0.4 - - + -
6007F G 4.0 22.7 - - + +
6008F C 4.3 5.2 + - - -
5118K ARG* 2.7 52.9 + - - +
5119K SER* 1.3 73.9 + - - +
5121K GLU* 1.3 65.4 + - - +
5123K THR* 3.3 9.7 + - - -
5124K ARG* 3.1 23.6 + - - +
6118L ARG* 4.0 10.9 + - - +
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Residues in contact with GLU5121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5004E G 5.0 0.6 + - - -
5005E G 3.5 22.6 + - + +
5006E C 3.3 43.6 + - + +
5116K PHE* 3.5 22.1 - - + +
5117K SER* 3.5 13.1 + - - -
5118K ARG* 3.0 38.1 + - + +
5120K ASP* 1.3 79.4 - - - +
5122K LEU* 1.3 57.3 + - - +
5124K ARG* 3.5 25.4 + - - +
5125K HIS* 3.1 26.3 + - - +
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Residues in contact with LEU5122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5105K TYR* 3.8 23.3 - - + -
5106K ALA 3.4 24.9 - - - +
5107K CYS* 3.7 17.7 - - + +
5108K PRO* 4.6 1.6 - - + -
5116K PHE* 3.5 34.5 - - + -
5118K ARG 3.5 1.6 + - - -
5119K SER 3.2 9.0 + - - +
5121K GLU* 1.3 79.5 - - - +
5123K THR* 1.3 60.7 + - - +
5125K HIS* 3.2 12.9 + - + -
5126K ILE* 2.9 37.4 + - + +
6097L TYR* 5.3 1.3 - - + +
6099L VAL* 3.6 26.9 - - + -
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Residues in contact with THR5123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5119K SER* 3.1 16.9 + - - -
5120K ASP* 3.3 11.6 + - - -
5122K LEU* 1.3 78.0 - - - +
5124K ARG* 1.3 62.1 + - - +
5126K ILE* 3.6 14.1 + - + +
5127K ARG* 3.7 28.1 + - - +
6097L TYR 5.9 3.1 - - - +
6098L VAL* 6.2 2.5 - - - -
6099L VAL* 3.5 20.0 + - + +
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Residues in contact with ARG5124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5004E G 3.4 24.7 + - - +
5005E G 3.0 48.9 + - - -
5006E C 3.6 11.7 - - - +
6009F G 3.7 7.8 + - - -
6010F C 4.8 0.2 - - - +
5116K PHE* 6.1 0.6 - - - -
5120K ASP 3.1 16.0 + - - +
5121K GLU* 3.6 20.0 + - - +
5123K THR* 1.3 75.8 - - - +
5125K HIS* 1.3 63.9 + - - +
5127K ARG* 3.1 43.2 + - - +
5128K ILE* 4.0 3.6 + - - +
5145K SER* 6.0 0.2 - - - -
5146K ARG* 3.4 55.9 - - + +
5148K ASP* 5.7 0.8 + - - -
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Residues in contact with HIS5125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5004E G 2.8 34.4 + - - +
5107K CYS* 3.6 3.3 - - + +
5112K CYS* 3.4 10.0 - - - -
5114K ARG* 3.9 13.3 - - + +
5116K PHE* 3.5 18.6 - + + -
5121K GLU 3.1 11.9 + - - +
5122K LEU* 3.5 28.5 - - + +
5124K ARG* 1.3 80.8 - - - +
5126K ILE* 1.3 63.0 + - - +
5128K ILE* 2.9 34.3 + - + +
5129K HIS* 3.4 11.0 - + - -
5201K ZN 2.0 36.6 - - - -
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Residues in contact with ILE5126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5107K CYS* 4.7 2.2 - - - -
5108K PRO* 3.9 17.0 - - + -
5122K LEU* 2.9 38.7 + - + +
5123K THR* 3.8 9.2 - - + +
5124K ARG 3.3 0.4 - - - -
5125K HIS* 1.3 79.4 - - + +
5127K ARG* 1.3 60.6 + - + +
5128K ILE 3.2 0.9 + - - -
5129K HIS* 3.3 19.3 + - + +
5130K THR* 3.3 13.4 + - + +
6094L LEU* 3.5 32.3 - - + +
6097L TYR* 3.6 36.6 - - + +
6099L VAL* 4.4 5.4 - - + -
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Residues in contact with ARG5127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5123K THR* 3.7 23.5 + - - +
5124K ARG* 3.1 44.2 + - - +
5125K HIS 3.0 1.2 - - - -
5126K ILE* 1.3 75.6 - - + +
5128K ILE* 1.3 59.6 + - - +
5130K THR* 3.5 7.9 - - - -
5131K GLY* 2.9 23.9 + - - -
5132K GLN* 3.3 45.2 + - + +
5134K PRO* 4.1 19.8 - - - +
5135K PHE* 5.2 8.7 - - - -
5145K SER* 4.0 26.3 + - - -
5146K ARG* 5.3 3.6 - - - +
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Residues in contact with ILE5128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5003E G 3.6 60.1 - - + +
5004E G 3.8 15.3 - - - +
5124K ARG 5.0 2.0 - - - +
5125K HIS* 2.9 21.5 + - + +
5127K ARG* 1.3 77.7 - - - +
5129K HIS* 1.3 75.6 + - + +
5131K GLY* 3.0 15.6 + - - -
5145K SER* 6.0 3.8 - - - +
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Residues in contact with HIS5129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5107K CYS* 3.5 1.1 - - - -
5109K VAL* 3.5 29.0 - - + +
5111K SER* 5.8 0.4 - - - -
5112K CYS* 3.7 11.9 - - + -
5125K HIS* 3.0 22.9 + + - -
5126K ILE* 3.3 15.5 + - + +
5128K ILE* 1.3 84.0 - - + +
5130K THR* 1.3 59.6 + - - +
5131K GLY 3.6 0.3 + - - -
5201K ZN 2.0 37.3 - - - -
6094L LEU* 3.9 17.0 - - + +
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Residues in contact with THR5130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5126K ILE* 3.3 10.0 + - + +
5127K ARG* 3.4 15.9 + - - -
5129K HIS* 1.3 75.3 - - - +
5131K GLY* 1.3 61.4 + - - +
5132K GLN* 3.0 26.3 + - - +
6094L LEU* 3.5 40.6 - - + +
6095L LEU* 4.0 28.9 - - + +
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Residues in contact with GLY5131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5127K ARG 2.9 9.5 + - - -
5128K ILE* 3.0 10.8 + - - -
5129K HIS 3.3 0.4 - - - -
5130K THR* 1.3 78.0 - - - +
5132K GLN* 1.3 66.5 + - - +
5133K LYS* 3.7 13.4 + - - +
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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