Contacts of the helix formed by residues 108 - 120 (chain C) in PDB entry 4NFT
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 PRO 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C TYR* 3.9 15.5 - - + -
9C TYR* 3.6 52.0 - - + +
100C SER* 3.8 5.2 - - - +
106C GLN 3.9 0.4 - - - -
107C PHE* 1.3 88.7 - - + +
109C VAL* 1.3 65.3 + - - +
110C GLY 3.3 2.5 - - - +
111C ARG* 3.5 18.1 + - + +
112C ILE* 3.2 27.4 + - + +
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Residues in contact with VAL 109 (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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99C ARG* 3.8 32.5 - - + +
100C SER* 3.1 33.0 + - - +
103C ALA* 5.2 0.4 - - + -
105C LEU* 4.5 9.2 - - + -
107C PHE 3.7 6.7 - - - +
108C PRO* 1.3 71.7 - - - +
110C GLY* 1.3 57.5 + - - +
112C ILE* 3.4 4.8 + - - -
113C HIS* 2.9 27.6 + - - +
131C ALA* 3.7 20.8 - - + +
132C VAL* 4.0 20.9 - - + +
135C ALA* 4.1 15.7 - - + -
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Residues in contact with GLY 110 (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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99C ARG* 4.8 12.6 - - - +
100C SER* 5.0 0.4 + - - -
108C PRO 3.3 0.6 - - - -
109C VAL* 1.3 78.5 - - - +
111C ARG* 1.3 62.3 - - - +
113C HIS* 3.1 8.4 + - - +
114C ARG* 3.0 40.5 + - - +
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Residues in contact with ARG 111 (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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5C SER 2.3 38.8 + - - +
6C TYR* 4.2 23.5 - - - +
8C ILE* 5.7 0.4 - - - +
9C TYR* 3.4 37.1 + - - -
108C PRO* 3.5 19.2 + - + +
109C VAL 3.5 0.2 - - - -
110C GLY* 1.3 75.1 - - - +
112C ILE* 1.3 57.5 + - + +
114C ARG* 3.2 32.0 + - + +
115C HIS* 2.9 30.2 + - + +
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Residues in contact with ILE 112 (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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6C TYR* 4.0 19.7 - - + +
39C PHE* 3.6 26.1 - - + -
107C PHE* 4.4 4.9 - - + -
108C PRO* 3.2 33.9 + - + +
109C VAL* 3.8 3.8 - - - +
111C ARG* 1.3 75.0 - - - +
113C HIS* 1.3 64.4 + - - +
115C HIS* 3.4 0.7 + - - -
116C LEU* 3.0 25.4 + - + +
131C ALA* 3.9 13.7 - - - +
134C SER* 3.9 23.3 - - - -
135C ALA* 3.7 27.8 - - + -
138C LEU* 4.4 12.3 - - + -
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Residues in contact with HIS 113 (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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99C ARG* 3.6 24.7 + - - +
109C VAL 2.9 15.2 + - - +
110C GLY* 3.1 11.4 + - - +
112C ILE* 1.3 78.3 - - - +
114C ARG* 1.3 64.1 + - - +
116C LEU* 3.4 5.4 + - - +
117C LYS* 3.0 31.2 + - + +
126C VAL* 3.4 48.6 + - + +
127C GLY 4.1 5.4 + - - -
128C ALA* 5.1 0.8 - - - -
131C ALA* 3.8 13.9 - - + +
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Residues in contact with ARG 114 (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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110C GLY* 3.0 29.0 + - - +
111C ARG* 3.2 43.3 + - + +
113C HIS* 1.3 78.1 - - - +
115C HIS* 1.3 57.6 + - - +
117C LYS* 3.0 23.9 + - - +
118C SER* 3.1 13.0 + - - -
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Residues in contact with HIS 115 (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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6C TYR* 5.4 2.0 - - - +
39C PHE* 3.3 36.5 - + + -
40C GLU* 5.0 5.8 - - + -
43C ALA* 4.4 6.2 - - + +
111C ARG* 2.9 18.0 + - + +
112C ILE 4.0 0.2 - - - +
113C HIS 3.4 0.2 - - - -
114C ARG* 1.3 73.1 - - - +
116C LEU* 1.3 65.7 + - - +
118C SER* 2.9 27.8 + - - -
119C ARG* 3.5 39.9 + - - +
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Residues in contact with LEU 116 (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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39C PHE* 4.2 9.2 - - + -
43C ALA* 4.0 25.4 - - + +
46C ALA* 5.5 0.2 - - + -
58C ILE* 4.0 19.1 - - + +
63C ILE* 4.1 19.5 - - + -
112C ILE* 3.0 25.0 + - + +
113C HIS 3.7 4.3 - - - +
115C HIS* 1.3 75.8 - - - +
117C LYS* 1.3 64.8 + - - +
119C ARG* 3.0 22.1 + - - +
120C THR 3.6 2.4 + - - -
126C VAL* 3.7 27.5 - - + +
130C ALA* 4.3 6.1 - - + +
131C ALA* 4.1 19.5 - - + -
134C SER* 3.9 18.2 - - - +
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Residues in contact with LYS 117 (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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113C HIS* 3.0 25.4 + - + +
114C ARG* 3.0 17.6 + - - +
116C LEU* 1.3 75.9 - - - +
118C SER* 1.3 55.6 + - - +
120C THR* 2.8 37.6 + - + +
121C THR 4.1 1.1 + - - +
122C SER* 3.8 24.8 + - - +
123C HIS* 4.7 0.6 - - - +
124C GLY 3.2 24.3 + - - -
125C ARG* 4.6 7.0 - - - +
126C VAL* 3.5 16.5 - - + +
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Residues in contact with SER 118 (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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114C ARG 3.1 9.5 + - - -
115C HIS* 2.9 33.0 + - - -
117C LYS* 1.3 71.8 - - - +
119C ARG* 1.3 64.1 + - - +
120C THR 3.1 8.9 + - - +
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Residues in contact with ARG 119 (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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40C GLU* 3.2 46.1 + - - +
43C ALA* 3.9 19.1 - - + +
44C GLY* 3.7 20.4 - - - +
47C SER* 3.8 28.7 + - - -
58C ILE* 4.5 3.1 - - + -
115C HIS* 3.6 34.6 + - - +
116C LEU* 3.0 12.4 + - + +
118C SER* 1.3 80.7 + - - +
120C THR* 1.3 58.5 + - - +
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Residues in contact with THR 120 (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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47C SER* 5.2 1.5 - - - -
56C SER* 3.5 23.2 + - - -
58C ILE* 4.2 11.4 - - - +
116C LEU 4.2 5.2 - - - -
117C LYS* 2.8 39.3 + - + +
118C SER* 3.6 6.9 - - - +
119C ARG* 1.3 82.9 - - - +
121C THR* 1.3 89.5 + - - +
124C GLY* 3.6 26.7 - - - -
125C ARG 4.0 6.0 + - - +
126C VAL* 5.1 0.2 - - - -
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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