Contacts of the helix formed by residues 116 - 128 (chain C) in PDB entry 3P3W
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 ALA 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C PRO* 5.1 7.9 - - + -
115C PRO* 1.3 71.2 - - - +
117C LEU* 1.3 63.3 + - - +
118C LYS* 3.3 4.7 - - + +
119C GLY* 3.8 13.3 + - - +
120C ALA 4.4 1.4 + - - -
349C ARG* 6.0 8.7 - - + +
350C ARG* 5.0 4.8 - - - +
353C TYR* 3.5 28.4 + - + +
355C ILE* 3.8 15.0 - - - +
373C GLU* 5.1 0.9 - - - +
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Residues in contact with LEU 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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102C PRO* 5.0 13.4 - - + +
114C ARG* 4.6 25.6 - - - +
115C PRO 3.3 7.1 + - - +
116C ALA* 1.3 70.3 - - - +
118C LYS* 1.3 64.3 + - - +
119C GLY 3.3 0.7 + - - -
120C ALA* 3.7 7.7 + - - +
121C ILE* 3.3 25.1 - - + +
141C ARG* 5.6 9.0 - - + -
145C VAL* 5.1 14.1 - - + -
192C ASP* 5.4 4.5 - - - +
220C ALA* 3.9 28.5 - - + +
221C ASN* 4.5 4.7 - - - +
222C LEU* 3.7 39.0 - - + +
242C PHE* 5.7 4.5 - - + -
355C ILE* 5.4 3.1 - - - -
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Residues in contact with LYS 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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116C ALA* 3.3 5.1 - - + -
117C LEU* 1.3 80.3 - - - +
119C GLY* 1.3 64.1 + - - +
120C ALA 3.6 0.2 + - - -
121C ILE* 3.7 13.5 + - - +
122C LEU* 3.9 24.3 - - + +
144C SER* 3.9 23.3 - - - +
145C VAL* 4.9 17.7 - - + +
148C ALA* 3.7 32.9 - - + +
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Residues in contact with GLY 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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116C ALA* 3.8 12.3 + - - +
117C LEU 3.3 1.4 - - - -
118C LYS* 1.3 81.9 - - - +
120C ALA* 1.3 62.8 + - - +
121C ILE 3.2 1.0 + - - -
122C LEU* 3.3 21.3 + - - +
123C SER* 4.1 4.0 + - - -
371C TRP* 3.8 26.8 - - - -
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Residues in contact with ALA 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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116C ALA 4.4 1.4 + - - -
117C LEU 3.7 7.4 + - - +
118C LYS 3.6 0.6 - - - -
119C GLY* 1.3 74.8 - - - +
121C ILE* 1.3 63.2 + - + +
122C LEU 3.5 0.2 + - - -
123C SER* 3.6 3.6 + - - -
124C LEU* 3.3 26.6 + - + +
242C PHE* 4.1 24.0 - - + -
355C ILE* 4.3 23.8 - - + -
357C VAL* 5.7 0.2 - - + -
371C TRP* 4.0 29.3 + - + -
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Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 3.3 23.6 - - + +
118C LYS* 3.9 8.7 - - - +
119C GLY 3.2 0.4 + - - -
120C ALA* 1.3 77.8 - - + +
122C LEU* 1.3 64.2 + - + +
123C SER 3.2 1.4 + - - -
124C LEU* 4.6 4.3 - - - +
125C LEU* 3.3 47.6 + - + +
145C VAL* 5.3 10.5 - - + -
149C ILE* 4.6 8.5 - - + -
190C LEU* 4.4 18.6 - - + -
218C MET* 4.7 7.9 - - - -
220C ALA* 4.0 27.4 - - + -
242C PHE* 4.2 24.7 - - + -
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Residues in contact with LEU 122 (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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118C LYS* 3.9 37.7 - - + +
119C GLY* 3.3 11.4 + - - +
121C ILE* 1.3 77.5 - - + +
123C SER* 1.3 60.7 + - - +
125C LEU* 4.7 6.9 - - + +
126C SER* 4.8 8.1 + - - -
148C ALA* 3.5 29.2 - - + +
149C ILE* 5.6 4.9 - - + -
152C ALA* 3.8 18.6 - - + -
156C ASN* 5.8 1.7 + - - -
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Residues in contact with SER 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLY 4.1 4.3 + - - -
120C ALA 3.6 3.6 + - - -
121C ILE 3.2 0.4 - - - -
122C LEU* 1.3 79.6 + - - +
124C LEU* 1.3 63.8 + - - +
125C LEU 3.3 2.2 - - - -
126C SER* 3.4 15.0 + - - -
127C TYR* 3.5 11.4 + - - +
371C TRP* 3.8 30.6 + - - -
376C ARG* 4.8 4.0 - - - -
377C PHE* 4.8 13.7 - - - +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ALA* 3.3 18.0 + - + +
121C ILE* 3.4 4.7 + - - +
123C SER* 1.3 76.4 - - - +
125C LEU* 1.3 61.2 + - + +
126C SER 3.3 1.1 - - - -
127C TYR* 3.5 11.4 + - + +
128C TYR* 3.2 50.8 - - + -
218C MET* 4.1 14.4 - - + -
240C THR* 4.0 17.7 - - + -
242C PHE* 3.6 29.8 - - + -
357C VAL* 3.7 25.1 - - + -
371C TRP* 6.3 1.8 - - + -
377C PHE* 4.2 21.7 - - + +
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Residues in contact with LEU 125 (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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121C ILE* 3.3 35.9 + - + +
122C LEU* 5.3 6.3 - - + +
123C SER 3.3 0.2 - - - -
124C LEU* 1.3 77.4 - - - +
126C SER* 1.3 57.9 + - - +
127C TYR 3.4 0.2 - - - -
128C TYR* 3.8 3.2 + - - -
129C LYS* 3.4 3.5 + - - -
130C TRP* 3.2 68.6 + - + +
133C PHE* 4.2 24.9 - - + -
149C ILE* 4.3 10.5 - - + -
190C LEU* 4.8 3.6 - - + -
218C MET* 3.7 21.3 - - + -
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Residues in contact with SER 126 (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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122C LEU 4.8 7.5 + - - -
123C SER* 3.4 11.8 + - - -
124C LEU 3.3 0.8 - - - -
125C LEU* 1.3 75.9 - - - +
127C TYR* 1.3 62.8 + - - +
128C TYR 3.2 1.8 - - - -
129C LYS* 3.4 29.9 + - - +
156C ASN* 5.8 5.7 + - - -
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Residues in contact with TYR 127 (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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123C SER 3.5 11.4 + - - +
124C LEU* 3.8 14.4 - - + +
125C LEU 3.4 0.4 - - - -
126C SER* 1.3 78.2 - - - +
128C TYR* 1.3 73.9 + + + +
129C LYS* 3.5 8.6 + - - +
377C PHE* 3.9 41.7 - + + -
379C PRO* 3.4 25.7 - - + +
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Residues in contact with TYR 128 (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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124C LEU* 3.2 46.8 + - + +
125C LEU* 3.8 2.2 + - - +
126C SER 3.2 0.2 - - - -
127C TYR* 1.3 95.9 - + - +
129C LYS* 1.3 68.0 + - - +
130C TRP* 3.5 36.7 + + + -
216C HIS* 3.7 23.9 - + - -
218C MET* 5.0 4.9 - - + -
240C THR* 3.8 19.9 + - - +
359C GLU* 5.0 10.9 - - - +
361C LYS* 5.4 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