Contacts of the helix formed by residues 116 - 129 (chain D) in PDB entry 2R2N
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D THR* 2.6 35.1 + - - -
115D SER* 1.3 75.1 - - - +
117D SER* 1.3 62.7 + - - -
118D GLN 3.3 1.6 - - - -
119D GLN 3.4 4.7 + - - -
262D SER* 5.3 0.2 - - - -
270D ARG* 3.2 34.6 + - - -
271D ILE 3.9 1.6 - - - -
272D GLY 3.8 9.2 - - - -
426D PMP 3.7 1.6 - - - -
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Residues in contact with SER 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D THR* 3.9 5.8 - - - -
116D GLY* 1.3 70.2 - - - -
118D GLN* 1.3 67.0 + - - +
119D GLN 3.1 0.9 + - - -
120D GLY* 3.1 4.9 + - - -
121D LEU* 3.1 21.9 + - - +
230D ASP* 4.5 4.5 + - - -
232D PRO* 4.8 0.9 - - - +
258D ALA* 4.3 15.1 - - - +
259D ASP 3.3 31.2 - - - -
260D SER* 3.8 4.9 - - - -
272D GLY* 3.8 3.6 - - - -
273D PHE 4.9 1.1 - - - +
426D PMP 2.9 41.4 + - - -
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Residues in contact with GLN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C GLN 4.0 1.0 + - - -
290C VAL* 3.4 25.1 + - - +
291C SER 3.3 16.2 - - - +
293C LEU* 3.7 19.9 - - + +
117D SER* 1.3 78.8 + - - +
119D GLN* 1.3 57.1 + - - +
121D LEU* 3.7 15.0 - - - +
122D CYS* 2.7 28.8 + - - +
142D TYR* 3.3 36.5 + - - -
144D GLY* 4.0 20.8 + - - -
145D THR* 4.8 2.7 - - - +
148D SER* 5.9 1.3 - - - -
426D PMP 3.0 25.9 + - - +
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Residues in contact with GLN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C SER* 3.2 24.0 + - - +
292C THR* 3.9 7.1 - - + +
114D THR* 3.6 8.1 - - - -
115D SER* 2.8 49.0 + - - +
116D GLY 3.4 5.3 + - - +
117D SER 3.1 1.4 + - - -
118D GLN* 1.3 77.2 - - - +
120D GLY* 1.3 56.6 + - - +
122D CYS* 3.3 1.7 + - - +
123D LYS* 2.9 49.8 + - + +
288D ILE* 3.7 22.1 - - + +
291D SER* 4.3 1.0 + - - -
292D THR* 2.9 38.9 + - - +
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Residues in contact with GLY 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D THR* 3.9 25.5 - - - -
117D SER 3.1 6.7 + - - -
119D GLN* 1.3 79.0 - - - +
121D LEU* 1.3 61.0 + - - +
123D LYS* 3.3 1.7 + - - +
124D VAL* 3.0 28.6 + - - +
274D LEU* 3.9 21.5 - - - +
284D VAL* 4.8 4.9 - - - -
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D SER 3.1 20.2 + - - +
118D GLN* 3.7 24.0 - - - +
120D GLY* 1.3 75.3 - - - +
122D CYS* 1.3 65.1 + - - +
124D VAL* 3.2 6.4 + - - +
125D PHE* 2.9 38.9 + - + -
145D THR* 4.9 5.2 - - + -
195D TYR* 4.3 3.1 - - + -
228D ILE* 3.1 35.2 - - + -
230D ASP* 3.3 42.6 - - + +
258D ALA* 3.9 16.4 - - + -
274D LEU* 4.7 2.6 - - + +
426D PMP 4.2 5.2 - - + -
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Residues in contact with CYS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ARG* 6.1 0.2 - - - -
123C LYS* 5.5 0.2 - - - -
287C HIS* 4.6 2.9 - - - -
290C VAL* 3.3 35.4 - - - +
291C SER* 3.8 19.3 - - - -
118D GLN* 2.7 17.3 + - - +
119D GLN 3.6 4.0 - - - +
121D LEU* 1.3 75.3 - - - +
123D LYS* 1.3 63.4 + - + +
125D PHE* 3.3 10.7 + - - +
126D GLU* 3.1 51.5 + - - +
148D SER* 4.0 12.3 - - - +
152D LEU* 6.6 0.2 - - - -
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Residues in contact with LYS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C CYS* 5.6 0.2 - - - -
123C LYS* 4.3 16.2 - - - +
126C GLU* 5.4 0.6 + - - -
291C SER* 5.3 2.8 - - - -
119D GLN* 2.9 47.3 + - + +
120D GLY 4.0 0.2 - - - +
122D CYS* 1.3 76.5 - - + +
124D VAL* 1.3 57.4 + - - +
126D GLU* 3.4 18.6 + - - +
127D MET* 2.9 30.1 + - - +
284D VAL* 3.9 32.8 - - + +
287D HIS* 3.6 33.7 + - + +
288D ILE* 4.0 10.8 - - + -
291D SER* 2.9 35.0 + - - -
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D GLY 3.0 21.5 + - - +
121D LEU* 3.5 7.6 - - - +
123D LYS* 1.3 74.3 - - - +
125D PHE* 1.3 69.3 + - + +
127D MET* 3.2 9.3 + - + +
128D ILE* 3.2 44.3 + - + +
228D ILE* 4.4 19.5 - - + -
256D ILE* 3.9 38.4 - - + -
274D LEU* 3.9 14.6 - - + -
284D VAL* 4.3 9.4 - - + -
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Residues in contact with PHE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LEU* 2.9 32.5 + - + -
122D CYS* 3.7 4.3 - - - +
124D VAL* 1.3 78.2 - - + +
126D GLU* 1.3 58.0 + - - +
128D ILE* 3.3 2.1 + - - -
129D ILE* 3.0 39.1 + - + +
145D THR* 4.2 19.3 - - + -
148D SER* 3.4 26.0 - - - +
149D LEU* 3.6 24.0 - - + -
152D LEU* 3.7 18.6 - - + +
193D PHE* 3.8 26.0 - + - -
195D TYR* 4.0 25.8 - + - -
228D ILE* 3.9 23.1 - - + -
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Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ARG* 4.6 3.3 + - - -
126C GLU* 5.5 0.7 - - - -
287C HIS* 2.9 32.3 + - - -
8D THR* 4.0 16.6 + - - +
11D SER* 5.1 0.2 - - - -
122D CYS* 3.1 30.2 + - - +
123D LYS* 3.5 15.9 + - - +
124D VAL 3.2 0.2 - - - -
125D PHE* 1.3 75.8 - - - +
127D MET* 1.3 61.9 - - - +
128D ILE 3.5 0.2 + - - -
129D ILE 4.2 6.2 + - - +
152D LEU* 4.6 23.5 - - + +
287D HIS* 3.1 33.2 - - + -
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Residues in contact with MET 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PHE 4.0 6.7 - - - +
7D ILE* 3.4 3.8 - - + -
8D THR* 2.8 33.5 + - - -
11D SER* 3.4 26.9 - - - +
123D LYS 2.9 18.1 + - - +
124D VAL* 3.2 10.7 + - + +
126D GLU* 1.3 79.1 - - - +
128D ILE* 1.3 84.3 + - + +
256D ILE* 4.2 9.6 - - + -
280D LEU* 3.5 39.7 - - + +
283D ARG* 3.5 27.4 - - + -
284D VAL* 4.7 5.8 - - - +
287D HIS* 5.7 0.4 + - - -
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PHE* 3.3 26.9 - - + +
7D ILE 5.1 0.3 - - - -
8D THR* 4.2 7.5 + - - -
124D VAL* 3.2 37.3 + - + +
125D PHE 4.0 1.3 - - - +
127D MET* 1.3 89.3 - - + +
129D ILE* 1.3 66.2 + - + +
130D ASN* 3.6 1.7 + - - -
192D LYS* 3.6 52.5 + - + -
193D PHE* 3.9 23.8 - - + -
226D LEU* 3.7 25.4 - - + -
228D ILE* 4.9 1.8 - - + -
256D ILE* 4.6 0.7 - - + -
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Residues in contact with ILE 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D THR* 3.8 7.9 + - - -
125D PHE* 3.0 18.7 + - + +
126D GLU* 4.2 5.6 + - - +
127D MET 3.8 0.6 - - - -
128D ILE* 1.3 77.2 - - + +
130D ASN* 1.3 75.1 + - - +
131D PRO* 4.6 1.4 - - - +
133D ASP* 3.8 6.1 - - + +
135D VAL* 4.3 7.2 - - + -
149D LEU* 3.5 32.5 - - + -
152D LEU* 3.7 38.1 - - + +
154D CYS* 3.7 24.0 - - + -
192D LYS* 6.0 0.2 - - + -
193D PHE* 3.8 27.4 - - + -
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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