Contacts of the helix formed by residues 116 - 129 (chain C) in PDB entry 3DC1
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 116 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C THR* 2.8 20.4 + - - -
115C SER* 1.3 77.3 - - - +
117C SER* 1.3 67.4 + - - -
118C GLN 2.9 5.5 + - - -
119C GLN* 3.0 8.0 + - - +
262C SER* 5.2 0.9 - - - -
263C LLP 3.4 2.7 - - - -
270C ARG* 3.4 27.5 - - - -
271C ILE 3.9 4.5 - - - -
272C GLY 3.2 13.0 - - - +
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Residues in contact with SER 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR* 4.0 7.8 + - - -
116C GLY* 1.3 71.2 - - - -
118C GLN* 1.3 57.4 + - - +
119C GLN 3.2 0.6 + - - -
120C GLY* 3.3 3.8 + - - -
121C LEU* 3.0 24.6 + - - +
230C ASP* 4.1 10.7 + - - -
232C PRO* 4.9 0.2 - - - +
258C ALA* 4.3 7.4 - - - +
259C ASP 3.2 37.7 - - - -
260C SER* 3.8 5.3 + - - -
263C LLP 2.9 35.6 + - - -
272C GLY* 3.8 4.4 - - - -
273C PHE 4.6 1.6 - - - +
274C LEU* 5.2 0.5 - - - +
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Residues in contact with GLN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLY 2.9 0.6 + - - -
117C SER* 1.3 78.7 + - - +
119C GLN* 1.3 60.2 + - - +
121C LEU* 3.4 22.6 - - + +
122C CYS* 2.8 30.1 + - - +
142C TYR* 3.1 33.9 + - - -
144C GLY* 5.2 5.5 - - - -
263C LLP 2.5 55.4 + - + +
289D GLN 4.9 3.4 + - - -
290D VAL* 3.7 8.7 + - - +
291D SER 3.2 14.6 - - - +
293D LEU* 3.5 26.8 - - + +
426D GOL 3.9 2.6 + - - -
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Residues in contact with GLN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR* 3.8 8.2 - - - -
115C SER* 2.9 37.0 + - - +
116C GLY 3.0 12.5 + - - +
118C GLN* 1.3 79.3 - - - +
120C GLY* 1.3 60.4 + - - +
122C CYS* 3.3 3.1 + - - +
123C LYS* 3.2 50.3 + - + +
288C ILE* 4.1 11.4 - - - +
292C THR* 2.8 41.6 + - - +
294C HIS 6.2 0.2 - - - -
295C PRO* 5.8 0.2 - - - +
123D LYS* 6.0 0.4 - - - +
291D SER* 3.2 16.9 + - - +
292D THR* 3.6 13.0 - - + +
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Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR* 3.8 25.8 - - - -
117C SER 3.3 5.8 + - - -
119C GLN* 1.3 78.6 - - - +
121C LEU* 1.3 62.8 + - - +
123C LYS* 4.0 1.1 - - - +
124C VAL* 3.1 30.3 + - - +
274C LEU* 4.0 17.7 - - - +
284C VAL* 4.8 6.2 - - - +
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Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C SER 3.0 13.8 + - - +
118C GLN* 3.4 26.5 - - + +
120C GLY* 1.3 75.5 - - - +
122C CYS* 1.3 61.3 + - - +
124C VAL* 3.3 13.8 + - - +
125C PHE* 3.3 35.6 + - + -
142C TYR* 5.9 0.9 - - + -
145C THR* 4.0 19.7 - - - +
148C SER* 6.3 0.2 - - - -
195C TYR* 4.0 7.6 - - + +
228C ILE* 4.2 14.8 - - + -
230C ASP* 3.7 42.8 - - + +
258C ALA* 4.1 12.1 - - + -
263C LLP 5.8 0.2 - - - +
274C LEU* 4.4 3.8 - - + +
290D VAL 6.2 0.4 - - - +
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Residues in contact with CYS 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 GLN 2.8 14.6 + - - +
119C GLN 3.6 5.4 - - - +
120C GLY 3.2 0.4 - - - -
121C LEU* 1.3 74.9 - - - +
123C LYS* 1.3 62.6 + - + +
125C PHE* 3.3 12.6 + - - +
126C GLU* 3.1 46.7 + - - +
148C SER* 4.2 11.2 - - - -
152C LEU* 6.4 0.7 - - - -
14D ARG* 6.0 0.2 - - - -
287D HIS* 4.4 3.6 - - - -
290D VAL* 3.2 37.5 - - - +
291D SER* 3.7 18.2 - - - -
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Residues in contact with LYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLN* 3.2 38.8 + - + +
120C GLY 3.6 0.6 + - - +
122C CYS* 1.3 76.8 - - + +
124C VAL* 1.3 57.6 + - - +
126C GLU* 3.6 12.8 - - - +
127C MET* 3.1 30.0 + - - +
284C VAL* 3.8 25.2 - - + +
287C HIS* 3.2 47.6 + - + +
288C ILE* 3.9 20.2 - - + -
291C SER* 3.2 30.0 + - - -
122D CYS* 5.5 0.2 - - - -
123D LYS* 4.8 13.6 - - - +
126D GLU* 5.8 0.2 + - - -
291D SER* 5.5 2.0 - - - -
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Residues in contact with VAL 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C GLY 3.1 19.4 + - - +
121C LEU* 3.5 7.0 - - - +
122C CYS 3.1 0.2 - - - -
123C LYS* 1.3 75.2 - - - +
125C PHE* 1.4 65.1 + - - +
127C MET* 3.2 12.3 - - + +
128C ILE* 3.0 44.6 + - + +
228C ILE* 3.8 21.8 - - + -
256C ILE* 3.8 24.7 - - + -
274C LEU* 3.7 23.1 - - + -
284C VAL* 4.1 8.5 - - + -
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Residues in contact with PHE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 3.3 38.5 + - + -
122C CYS* 3.3 8.7 + - - +
124C VAL* 1.4 76.0 - - - +
126C GLU* 1.3 57.3 + - - +
128C ILE* 4.6 2.5 - - - -
129C ILE* 3.0 43.2 + - + +
145C THR* 3.9 28.0 - - + -
148C SER* 3.8 28.5 - - - -
149C LEU* 3.6 27.8 - - + -
152C LEU* 3.5 17.7 - - + -
193C PHE* 3.9 11.9 - + - -
195C TYR* 4.2 11.4 - + - -
228C ILE* 3.8 22.2 - - + -
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Residues in contact with GLU 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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8C THR* 3.4 14.6 + - - +
11C SER* 4.8 2.2 - - - -
122C CYS* 3.1 27.7 + - - +
123C LYS* 3.6 15.1 + - - +
124C VAL 3.2 0.4 - - - -
125C PHE* 1.3 73.4 - - - +
127C MET* 1.3 64.1 + - - +
129C ILE 4.4 3.5 + - - +
152C LEU* 4.0 23.6 - - + -
287C HIS* 2.8 34.4 + - + -
14D ARG* 4.5 4.9 + - - -
126D GLU* 4.8 1.9 - - - +
287D HIS* 2.9 33.8 + - - -
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Residues in contact with MET 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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6C PHE 3.9 0.9 - - - +
7C ILE* 3.3 16.7 - - - -
8C THR* 2.5 36.6 + - - -
11C SER* 3.5 21.3 - - - +
123C LYS 3.1 15.3 + - - +
124C VAL* 3.2 26.7 - - + +
126C GLU* 1.3 77.4 - - - +
128C ILE* 1.3 66.9 + - + +
256C ILE* 4.7 4.5 - - + -
280C LEU* 3.7 37.5 - - + +
283C ARG* 3.4 34.8 - - + +
284C VAL* 4.5 7.6 - - + -
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Residues in contact with ILE 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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5C ARG 4.9 0.7 - - - +
6C PHE* 3.4 29.3 - - + +
7C ILE 4.5 0.3 + - - -
8C THR* 3.9 3.9 + - - -
124C VAL* 3.0 40.6 - - + +
125C PHE 3.1 4.0 + - - +
127C MET* 1.3 87.4 - - + +
129C ILE* 1.3 64.9 - - + +
130C ASN* 3.8 5.0 + - - -
192C LYS* 3.7 34.6 + - + -
193C PHE* 3.5 37.2 - - + -
226C LEU* 3.8 23.3 - - + -
228C ILE* 4.3 3.4 - - + -
256C ILE* 4.4 3.8 - - + -
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Residues in contact with ILE 129 (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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8C THR* 3.7 10.3 + - - +
125C PHE* 3.0 17.3 + - + +
126C GLU* 4.5 3.5 - - - +
127C MET 3.6 0.8 - - - -
128C ILE* 1.3 76.3 - - + +
130C ASN* 1.4 74.3 + - - +
131C PRO* 4.6 2.3 - - - +
133C ASP* 3.8 7.0 - - + +
135C VAL* 4.5 5.6 - - + -
149C LEU* 3.5 31.9 - - + -
152C LEU* 3.7 43.3 - - + +
154C CYS* 3.9 23.3 - - + -
192C LYS* 5.8 0.2 - - + -
193C PHE* 3.8 24.9 - - + -
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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
------------------------------------------------------------
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