Contacts of the helix formed by residues 202 - 215 (chain K) in PDB entry 1P7G
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 ASN 202 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95K PRO 3.2 12.5 - - - +
96K ASN 2.8 22.6 + - - +
97K MSE 3.4 19.6 - - - +
98K ALA* 3.8 11.9 - - + +
102K LYS* 4.0 27.9 + - - +
103K GLY* 4.2 0.9 - - - -
200K VAL 3.2 2.4 + - - -
201K VAL* 1.3 69.6 - - - +
203K TRP* 1.3 57.3 + - - +
204K ASP* 3.2 23.2 + - - +
205K ASP* 2.9 34.0 + - - +
206K VAL* 3.2 7.8 + - - +
208K ARG* 4.8 4.2 + - - +
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Residues in contact with TRP 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K LYS 4.7 2.6 + - - -
104K GLY 3.6 21.4 + - - -
105K GLY 3.1 20.1 + - - -
106K LYS 4.0 3.6 - - - +
107K PRO* 3.5 38.0 - - + -
108K GLY 5.2 1.6 - - - +
111K ILE* 4.2 13.9 - - + +
115K ILE* 4.2 5.4 - - + -
122K PHE* 3.4 26.0 - + - -
125K PHE* 3.7 25.6 - + - -
144K LEU* 5.3 0.4 - - + -
173K LEU* 3.8 22.7 - - + -
198K TRP* 3.9 9.1 + + - -
201K VAL* 3.0 32.4 + - + +
202K ASN* 1.3 71.4 - - - +
204K ASP* 1.3 58.0 + - - +
206K VAL* 3.6 26.1 - - + +
207K GLU* 2.8 29.5 + - - +
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Residues in contact with ASP 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K LYS* 4.3 21.7 - - - +
202K ASN* 3.1 13.5 + - - +
203K TRP* 1.3 78.7 - - - +
205K ASP* 1.3 59.1 + - - +
207K GLU* 3.4 8.2 + - - +
208K ARG* 3.0 42.0 + - - +
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Residues in contact with ASP 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K PRO* 3.4 29.1 - - - +
96K ASN* 2.8 29.7 + - - -
202K ASN* 2.9 20.1 + - - +
204K ASP* 1.3 78.5 - - - +
206K VAL* 1.3 63.2 + - - +
208K ARG* 3.1 32.5 + - - +
209K ARG* 2.9 51.7 + - - +
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Residues in contact with VAL 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K ASN* 3.9 5.8 - - - +
111K ILE* 3.9 25.1 - - + -
144K LEU* 4.6 1.1 - - + -
172K LEU* 3.9 33.4 - - + +
173K LEU* 3.9 29.4 - - + -
201K VAL* 4.4 0.7 - - + -
202K ASN 3.2 12.3 + - - +
203K TRP* 3.3 30.0 + - + +
205K ASP* 1.3 75.5 - - - +
207K GLU* 1.3 56.9 + - - +
209K ARG* 3.6 3.1 + - - +
210K LEU* 3.1 26.2 + - - +
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Residues in contact with GLU 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K GLY 4.4 1.1 - - - +
109K GLY* 3.6 8.6 - - - -
110K LYS* 2.9 38.5 + - - +
111K ILE* 3.0 34.6 + - + +
203K TRP 2.8 18.1 + - - +
204K ASP* 3.5 10.5 - - - +
205K ASP 3.1 0.4 - - - -
206K VAL* 1.3 75.6 - - - +
208K ARG* 1.3 62.1 + - + +
210K LEU* 3.3 4.4 + - - +
211K GLN* 2.9 31.8 + - - +
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Residues in contact with ARG 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G GLU* 6.3 3.1 - - - -
95K PRO* 5.5 2.4 - - - +
102K LYS* 6.0 2.6 - - - +
202K ASN* 4.8 4.9 + - - +
204K ASP* 3.0 45.6 + - - +
205K ASP* 3.1 37.0 + - - +
207K GLU* 1.3 79.0 - - + +
209K ARG* 1.3 62.0 - - + +
211K GLN* 3.0 23.1 + - - +
212K LYS* 3.2 12.1 + - - +
222K LEU* 4.6 23.4 + - - +
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Residues in contact with ARG 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K SER 4.6 1.0 + - - -
92K ILE* 4.0 25.1 - - - +
95K PRO* 3.4 25.1 - - - +
96K ASN* 4.0 3.4 - - - +
171K VAL 3.6 11.2 + - - -
172K LEU* 3.3 33.9 - - + -
205K ASP* 2.9 41.1 + - - +
206K VAL 3.9 3.6 - - - +
208K ARG* 1.3 75.6 - - + +
210K LEU* 1.3 63.0 + - - +
212K LYS* 3.3 6.1 + - - +
213K ALA* 3.1 22.2 + - - +
219K ALA* 2.9 48.1 + - + +
220K LEU* 4.2 8.1 - - - +
221K LYS 5.5 0.2 - - - +
222K LEU* 4.7 12.8 + - - +
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Residues in contact with LEU 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K LYS* 3.6 12.6 - - + -
111K ILE* 3.3 44.9 - - + +
114K LEU* 3.5 30.7 - - + -
146K TYR* 4.0 12.1 - - + -
153K LEU* 4.5 0.7 - - + -
172K LEU* 3.7 28.4 - - + +
206K VAL 3.1 15.1 + - - +
207K GLU* 3.5 9.9 - - - +
208K ARG 3.2 0.2 - - - -
209K ARG* 1.3 75.9 - - - +
211K GLN* 1.3 54.5 + - - +
213K ALA* 4.4 0.4 - - - -
214K LEU* 2.8 45.9 + - + +
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Residues in contact with GLN 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G GLN* 5.8 2.1 + - - -
134G LYS* 5.8 2.9 - - - +
110K LYS* 3.8 29.8 - - - +
207K GLU* 2.9 22.1 + - + +
208K ARG* 3.0 16.5 + - - +
210K LEU* 1.3 77.4 - - - +
212K LYS* 1.3 59.2 + - + +
214K LEU* 3.4 7.4 + - - +
215K ASN* 2.7 47.9 + - - +
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Residues in contact with LYS 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G ASP* 3.2 43.2 + - - +
208K ARG 3.2 11.8 + - - +
209K ARG* 3.6 6.7 - - - +
211K GLN* 1.3 79.2 - - + +
213K ALA* 1.3 55.0 + - - +
215K ASN* 2.7 26.5 + - - +
216K GLY 3.2 0.2 + - - -
217K GLN* 2.9 32.7 + - + +
218K ILE 3.2 29.3 + - - +
219K ALA* 4.2 5.8 - - - -
220K LEU 4.7 6.9 + - - -
221K LYS 4.9 3.8 + - - -
222K LEU* 3.2 28.1 + - - +
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Residues in contact with ALA 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J ILE* 5.4 2.0 - - - +
146K TYR* 3.5 49.0 - - + -
148K PRO* 5.8 0.2 - - - +
170K GLN* 4.4 10.3 - - + -
172K LEU* 4.3 7.2 - - + -
209K ARG 3.1 14.9 + - - +
210K LEU* 3.7 3.8 - - - +
212K LYS* 1.3 78.0 - - - +
214K LEU* 1.3 58.6 + - - +
216K GLY* 2.8 19.9 + - - -
217K GLN 3.5 14.0 + - - +
219K ALA* 5.1 0.4 - - + +
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Residues in contact with LEU 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K LYS* 3.6 39.7 - - + +
114K LEU* 3.6 28.7 - - + -
146K TYR* 3.8 23.1 + - + +
151K GLU* 5.2 3.8 - - - +
210K LEU* 2.8 43.5 + - + +
211K GLN* 3.6 11.2 - - - +
213K ALA* 1.3 73.3 - - - +
215K ASN* 1.3 63.5 + - - +
216K GLY 3.2 2.6 + - - -
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Residues in contact with ASN 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G LYS* 4.3 14.5 - - - +
189G ASP* 3.6 21.9 - - - +
191G GLY* 6.3 1.8 - - - -
195G ASP* 5.0 0.6 + - - -
211K GLN* 2.7 39.5 + - - +
212K LYS* 2.7 4.3 + - - +
214K LEU* 1.3 81.3 - - - +
216K GLY* 1.3 62.0 + - - +
217K GLN* 2.8 29.2 + - - +
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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