Contacts of the helix formed by residues 138 - 147 (chain C) in PDB entry 5F0L
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 GLU 138 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C LEU* 4.4 2.2 - - + -
84C GLU* 3.9 24.3 - - + +
85C SER* 3.7 41.6 - - - +
134C LEU 3.8 10.9 - - - +
135C ALA 3.2 13.2 + - - +
137C ASN* 1.3 77.4 - - - +
139C ARG* 1.3 65.7 + - - +
140C CYS* 3.2 18.2 + - - -
141C LEU* 3.4 9.0 + - - +
142C HIS* 3.7 11.1 - - - -
156C PRO* 5.5 1.9 - - - +
157C SER 3.5 15.4 + - - +
158C LYS 3.6 17.3 - - - +
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Residues in contact with ARG 139 (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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61C LYS* 5.7 8.9 - - - +
137C ASN 3.5 3.0 + - - -
138C GLU* 1.3 72.4 + - - +
140C CYS* 1.3 63.6 + - - +
141C LEU 3.2 0.3 + - - -
142C HIS* 3.3 33.5 + - - +
143C MET* 3.1 48.1 + - + +
147C ASP* 2.8 35.5 + - - -
154C TYR* 4.5 7.4 - - + -
155C THR 5.6 0.7 - - - +
156C PRO* 5.4 0.2 - - + -
157C SER* 3.2 41.6 + - - +
158C LYS* 4.9 8.5 - - + +
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Residues in contact with CYS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TRP* 4.0 12.9 - - + -
77C LEU* 3.8 8.4 - - + +
80C GLU* 4.0 19.5 - - + -
81C LEU* 3.6 37.9 - - - -
138C GLU* 4.1 9.9 - - - -
139C ARG* 1.3 77.9 - - - +
141C LEU* 1.3 59.5 + - - +
143C MET* 3.5 8.2 - - - +
144C PHE* 3.0 29.8 + - - +
154C TYR* 3.6 24.1 + - - +
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Residues in contact with LEU 141 (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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60C PHE* 4.7 6.3 - - + -
77C LEU* 3.9 20.9 - - + -
81C LEU* 5.2 2.2 - - + -
126C ILE* 4.3 5.2 - - + -
129C VAL* 3.9 22.9 - - + +
130C ALA* 3.8 25.8 - - + +
135C ALA* 3.7 29.8 - - + +
136C GLN* 4.0 11.2 - - + +
138C GLU 3.4 9.8 + - - +
139C ARG 3.3 0.8 - - - -
140C CYS* 1.3 79.5 - - - +
142C HIS* 1.3 63.0 + - + +
144C PHE* 3.5 1.4 + - - +
145C LEU* 3.0 52.2 + - + +
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Residues in contact with HIS 142 (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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59C ILE* 3.4 37.4 + - + +
60C PHE* 3.6 37.4 - + - -
61C LYS* 4.8 5.9 + - + -
136C GLN* 2.8 29.6 + - - -
137C ASN 4.6 2.2 + - - -
138C GLU 3.7 13.7 - - - -
139C ARG* 3.3 27.7 + - - +
141C LEU* 1.3 74.7 - - + +
143C MET* 1.3 67.7 + - - +
145C LEU* 4.5 3.6 - - - +
146C GLN* 2.9 35.2 + - + +
147C ASP* 3.6 2.2 + - - +
158C LYS* 5.3 6.2 - - - -
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Residues in contact with MET 143 (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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69C ARG* 3.6 3.3 + - - -
76C TRP* 3.8 19.5 - - + -
139C ARG* 3.1 41.6 + - + +
140C CYS 3.5 5.8 - - - +
142C HIS* 1.3 78.0 - - - +
144C PHE* 1.3 61.5 + - - +
147C ASP* 3.3 45.9 + - - +
149C ILE 5.2 0.2 - - - +
150C ILE* 4.2 13.5 - - + +
151C ASP* 3.8 32.8 - - + +
154C TYR* 3.4 38.4 - - + -
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Residues in contact with PHE 144 (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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51C ILE* 4.4 4.5 - - + -
67C VAL* 3.7 4.9 - - - +
69C ARG* 2.6 59.8 + - + +
73C ASP* 3.7 6.5 - - + -
74C PHE* 3.7 58.1 - + - -
76C TRP* 4.6 3.3 - + + -
77C LEU* 3.6 31.2 - - + -
126C ILE* 3.6 25.8 - - + -
140C CYS 3.0 18.6 + - - +
141C LEU 3.6 3.8 - - - +
142C HIS 3.2 0.2 - - - -
143C MET* 1.3 75.5 - - - +
145C LEU* 1.3 73.0 + - + +
150C ILE* 4.0 11.0 - - + -
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Residues in contact with LEU 145 (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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31C ILE* 3.8 29.8 - - + -
51C ILE* 3.8 25.9 - - + +
53C VAL* 3.9 14.4 - - + +
60C PHE* 3.7 26.5 - - + -
65C SER* 3.3 13.5 + - - -
67C VAL* 3.2 20.8 - - - +
126C ILE* 3.8 13.5 - - + -
130C ALA* 4.3 1.6 - - + -
141C LEU* 3.0 38.8 + - + +
142C HIS* 4.2 0.9 - - - +
144C PHE* 1.3 82.8 - - + +
146C GLN* 1.3 70.3 + - + +
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Residues in contact with GLN 146 (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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53C VAL* 4.0 16.2 - - - +
60C PHE* 3.9 16.7 - - + +
61C LYS* 3.4 13.3 + - - +
62C LEU* 3.0 64.6 + - + +
65C SER* 3.4 26.4 + - - +
67C VAL* 4.3 7.2 - - - +
142C HIS* 2.9 17.5 + - + +
145C LEU* 1.3 91.6 - - + +
147C ASP* 1.3 64.6 + - - +
148C GLU 4.0 0.9 + - - -
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Residues in contact with ASP 147 (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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67C VAL* 3.6 6.0 - - - +
69C ARG* 3.2 20.8 + - - -
139C ARG* 2.8 32.3 + - - -
142C HIS 3.6 2.6 + - - +
143C MET* 3.3 31.6 + - + +
146C GLN* 1.3 80.7 - - - +
148C GLU* 1.3 65.5 + - - +
149C ILE* 3.4 15.1 + - - +
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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