Contacts of the helix formed by residues 128 - 145 (chain C) in PDB entry 6DWM
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 GLY 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C LYS* 4.7 7.0 + - - -
126C ASP* 3.0 10.7 + - - -
127C SER* 1.3 82.1 - - - +
129C PRO* 1.3 75.6 - - - +
130C VAL 3.3 2.4 + - - -
131C TRP* 3.4 3.0 + - - -
132C ALA* 3.3 17.7 + - - +
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Residues in contact with PRO 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLY* 1.3 80.6 - - - +
130C VAL* 1.3 72.4 + - + +
132C ALA* 3.5 8.0 + - + +
133C ALA* 3.3 21.8 + - - +
136C ARG* 5.3 1.2 + - - -
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Residues in contact with VAL 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ASP* 3.3 21.3 - - - +
128C GLY 3.3 0.8 - - - -
129C PRO* 1.3 85.7 - - + +
131C TRP* 1.3 62.8 + - - +
133C ALA* 3.5 6.2 + - - +
134C ARG* 3.5 30.2 + - + +
306C LYS* 5.2 15.5 - - + +
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Residues in contact with TRP 131 (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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104C LYS* 4.5 15.3 - - + -
121C MET* 3.4 35.0 + - + +
126C ASP* 3.3 33.7 + - + +
127C SER* 3.7 25.1 - - - -
128C GLY 3.4 6.6 + - - +
129C PRO 3.3 0.2 - - - -
130C VAL* 1.3 76.5 - - - +
132C ALA* 1.3 91.5 + - + +
134C ARG* 3.0 23.5 + - - +
135C ARG* 3.0 38.1 + - - +
454C LYS* 3.4 28.0 - - + -
455C ARG* 3.4 42.8 - - - +
601C HEM 3.9 4.2 + - - -
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Residues in contact with ALA 132 (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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104C LYS* 6.1 1.1 - - - +
128C GLY 3.3 6.3 + - - +
129C PRO* 3.9 11.0 - - + +
130C VAL 3.4 0.2 - - - -
131C TRP* 1.3 102.7 - - + +
133C ALA* 1.3 61.0 + - - +
135C ARG* 3.4 7.4 + - - +
136C ARG* 3.2 34.4 + - - +
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Residues in contact with ALA 133 (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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129C PRO 3.3 10.9 + - - +
130C VAL* 3.8 10.3 - - - +
131C TRP 3.2 0.6 - - - -
132C ALA* 1.3 79.2 - - - +
134C ARG* 1.3 62.8 + - + +
136C ARG* 3.2 28.8 + - - +
137C LEU* 3.1 25.4 + - + +
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Residues in contact with ARG 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLN* 3.1 26.5 + - - +
120C SER 4.4 2.2 + - - -
121C MET* 3.3 41.1 - - + +
124C SER* 4.6 6.5 + - - -
126C ASP* 4.9 8.3 + - - +
130C VAL* 3.5 23.5 - - + +
131C TRP* 3.0 12.9 + - - +
133C ALA* 1.3 76.2 - - + +
135C ARG* 1.3 64.8 + - - +
137C LEU* 3.0 21.1 + - + +
138C ALA* 3.0 11.6 + - - +
306C LYS* 3.0 48.9 + - + +
307C ILE* 5.7 3.6 - - + -
309C ASN* 3.2 20.2 + - - -
310C ILE* 3.8 17.9 - - + +
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Residues in contact with ARG 135 (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 MET* 3.9 12.9 - - + -
131C TRP* 3.0 39.0 + - + +
132C ALA* 3.7 10.8 - - - +
133C ALA 3.3 0.4 - - - -
134C ARG* 1.3 77.1 - - - +
136C ARG* 1.3 57.0 + - + +
138C ALA* 3.2 4.8 + - - +
139C GLN* 3.0 44.2 + - - +
453C GLY 4.5 0.6 + - - -
454C LYS 3.4 17.0 + - - -
455C ARG 4.0 0.4 - - - -
456C LYS* 2.8 46.9 + - - +
457C CYS 4.5 0.4 + - - -
458C ILE* 3.1 34.8 - - + +
601C HEM 2.8 32.0 + - - +
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Residues in contact with ARG 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C PRO 5.3 0.8 + - - -
132C ALA* 3.2 17.3 + - - +
133C ALA* 3.2 40.1 + - - +
135C ARG* 1.3 74.8 - - + +
137C LEU* 1.3 59.4 + - - +
139C GLN* 3.8 16.6 - - - +
140C ASN* 2.9 45.6 + - - +
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Residues in contact with LEU 137 (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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133C ALA* 3.1 18.4 + - + +
134C ARG* 3.0 12.0 + - + +
136C ARG* 1.3 76.5 - - - +
138C ALA* 1.3 58.7 + - - +
140C ASN* 3.8 7.5 - - + +
141C GLY* 2.8 26.3 + - - -
281C ILE* 5.7 0.3 - - - +
284C SER 5.7 1.1 - - - +
285C LEU* 4.2 20.1 - - + +
288C HIS* 3.9 50.7 - - + +
307C ILE* 4.1 22.9 - - + -
310C ILE* 4.2 12.6 - - + -
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Residues in contact with ALA 138 (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 MET* 4.5 4.9 - - + -
134C ARG 3.0 8.5 + - - +
135C ARG 3.6 8.1 - - - +
136C ARG 3.2 0.2 - - - -
137C LEU* 1.3 74.5 - - - +
139C GLN* 1.3 59.6 + - - +
141C GLY* 3.2 1.2 + - - -
142C LEU* 2.8 37.5 + - - +
281C ILE* 6.1 0.4 - - - -
285C LEU* 6.1 0.2 - - - -
310C ILE* 3.7 26.2 - - + +
314C LEU* 4.1 12.7 - - + +
458C ILE* 3.6 24.0 - - + -
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Residues in contact with GLN 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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135C ARG* 3.0 43.8 + - - +
136C ARG* 3.8 20.7 - - + +
138C ALA* 1.3 74.3 - - - +
140C ASN* 1.3 62.5 + - - +
142C LEU* 3.8 6.8 - - - +
143C LYS* 2.8 33.5 + - - +
456C LYS* 4.9 9.3 - - - +
458C ILE* 4.1 26.1 - - + +
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Residues in contact with ASN 140 (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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136C ARG* 2.9 32.1 + - - +
137C LEU* 4.1 8.5 - - + +
139C GLN* 1.3 76.1 - - - +
141C GLY* 1.3 59.6 + - - +
143C LYS* 4.1 19.6 + - - +
144C SER* 2.5 40.6 + - - +
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Residues in contact with GLY 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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137C LEU 2.8 18.7 + - - -
138C ALA 3.7 0.9 - - - -
140C ASN* 1.3 78.0 - - - +
142C LEU* 1.3 60.9 + - - +
144C SER* 4.5 3.1 - - - -
145C PHE* 3.3 17.4 + - - -
281C ILE* 3.3 31.5 - - - +
284C SER* 4.3 15.3 - - - -
285C LEU* 6.4 0.4 - - - -
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Residues in contact with LEU 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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138C ALA 2.8 22.3 + - - +
139C GLN* 3.8 3.4 - - - +
141C GLY* 1.3 70.4 - - - +
143C LYS* 1.3 57.4 + - - +
145C PHE 3.1 2.4 + - - -
146C SER* 2.5 39.5 + - - -
198C ILE* 4.8 4.9 - - + -
201C ILE* 4.4 9.0 - - + -
281C ILE* 3.7 19.2 - - + +
314C LEU* 4.1 26.5 - - + -
458C ILE* 3.7 30.3 - - + +
459C GLY* 4.3 0.2 - - - -
462C ILE* 3.7 27.8 - - + -
601C HEM 4.0 23.6 - - + -
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Residues in contact with LYS 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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139C GLN 2.8 21.0 + - - +
140C ASN* 4.1 18.6 + - - +
142C LEU* 1.3 75.0 - - - +
144C SER* 1.3 67.9 + - - +
145C PHE 3.3 0.9 + - - -
146C SER* 3.7 6.1 - - - -
147C ILE* 3.4 25.1 + - + +
148C ALA* 3.4 20.6 + - - +
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Residues in contact with SER 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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140C ASN* 2.5 30.0 + - - +
141C GLY* 3.8 0.7 - - - -
143C LYS* 1.3 82.1 + - - +
145C PHE* 1.3 83.7 + - - +
148C ALA* 3.1 24.0 - - - +
158C TYR* 4.0 6.2 - - - -
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Residues in contact with PHE 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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141C GLY* 3.3 18.8 + - - +
142C LEU 3.1 4.4 + - - -
144C SER* 1.3 92.8 - - - +
146C SER* 1.3 59.1 + - - +
158C TYR* 3.5 40.9 - + + +
162C HIS* 4.8 0.3 - - - -
201C ILE* 3.6 36.2 - - + +
278C ILE* 3.5 27.4 - - + -
279C ARG 3.5 16.8 - - - -
280C ASP* 3.4 43.1 - - - -
281C ILE* 4.1 1.6 - - + -
284C SER* 4.1 15.3 - - - -
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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
------------------------------------------------------------
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