Contacts of the helix formed by residues 202 - 215 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95H PRO 3.4 24.0 - - - +
96H ASN 2.8 10.1 + - - +
97H MSE 3.7 15.8 - - - +
98H ALA* 3.7 19.4 - - - +
102H LYS* 5.2 6.8 + - - +
103H GLY* 4.8 3.9 - - - -
200H VAL 3.2 2.1 + - - -
201H VAL* 1.3 67.6 - - - +
203H TRP* 1.3 57.0 + - - +
204H ASP* 2.9 32.7 + - - +
205H ASP* 3.0 18.5 + - - +
206H VAL* 3.3 13.2 + - - +
208H ARG* 4.4 6.6 + - - -
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Residues in contact with TRP 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H GLY* 5.6 0.4 - - - -
104H GLY 4.8 1.0 - - - -
105H GLY 2.8 34.6 + - - +
107H PRO* 3.5 29.2 - - + -
108H GLY 5.4 0.9 - - - +
111H ILE* 4.1 9.4 - - + +
115H ILE* 4.0 17.0 - - + -
122H PHE* 3.5 25.2 - + - -
125H PHE* 3.8 19.5 - + - -
144H LEU* 5.2 0.4 - - + -
173H LEU* 3.7 26.2 - - + -
198H TRP* 3.9 12.5 + + - -
201H VAL* 3.2 34.4 + - + +
202H ASN* 1.3 70.8 - - - +
204H ASP* 1.3 57.3 - - - +
205H ASP 3.4 0.2 - - - -
206H VAL* 3.9 27.8 - - + +
207H GLU* 3.3 23.0 + - - +
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Residues in contact with ASP 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H ASN* 2.9 13.2 + - - +
203H TRP* 1.3 77.5 - - - +
205H ASP* 1.3 62.5 + - - +
207H GLU* 3.4 7.7 + - - +
208H ARG* 2.9 50.1 + - - +
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Residues in contact with ASP 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H PRO* 3.3 30.8 - - - +
96H ASN* 2.7 27.8 + - - +
202H ASN* 3.0 12.6 + - - +
204H ASP* 1.3 77.9 - - - +
206H VAL* 1.3 65.4 + - - +
208H ARG* 3.1 31.5 + - - +
209H ARG* 2.8 56.7 + - - +
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Residues in contact with VAL 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H ASN* 4.4 5.2 - - - +
111H ILE* 3.7 29.4 - - + -
144H LEU* 4.8 1.8 - - + -
172H LEU* 3.9 34.2 - - + +
173H LEU* 4.0 23.6 - - + -
201H VAL* 4.3 1.8 - - + -
202H ASN 3.5 15.7 - - - +
203H TRP* 3.9 28.7 - - + +
204H ASP 3.3 0.2 - - - -
205H ASP* 1.3 77.0 - - - +
207H GLU* 1.3 57.1 + - - +
209H ARG* 3.1 4.3 + - - +
210H LEU* 2.9 27.9 + - - +
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Residues in contact with GLU 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H GLY 4.4 0.4 - - - -
109H GLY* 3.0 12.6 - - - -
110H LYS* 2.6 35.9 + - - +
111H ILE* 2.6 36.9 + - + +
203H TRP 3.3 18.3 + - - +
204H ASP* 3.4 10.3 - - - +
205H ASP 3.2 0.2 - - - -
206H VAL* 1.3 79.8 - - - +
208H ARG* 1.3 64.7 + - + +
210H LEU* 3.3 3.8 + - - +
211H GLN* 3.0 26.7 + - + +
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Residues in contact with ARG 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LYS* 6.1 3.1 - - - +
37C GLU* 6.2 3.1 - - - -
95H PRO* 5.2 1.4 + - - +
202H ASN* 4.4 6.9 + - - -
204H ASP* 2.9 36.7 + - - +
205H ASP* 3.1 39.0 + - - +
207H GLU* 1.3 77.3 - - + +
209H ARG* 1.3 61.7 + - + +
211H GLN* 3.9 5.0 - - - +
212H LYS* 3.2 36.2 + - + +
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Residues in contact with ARG 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H ILE* 3.7 12.7 - - - +
95H PRO* 3.2 26.1 - - - +
96H ASN* 3.5 5.4 - - - +
171H VAL 3.7 11.7 - - - -
172H LEU* 3.5 29.2 - - + -
205H ASP* 2.8 47.1 + - - +
206H VAL 3.1 6.7 + - - +
208H ARG* 1.3 75.9 - - + +
210H LEU* 1.3 65.0 + - - +
212H LYS* 3.4 5.6 + - + +
213H ALA* 3.0 19.2 + - - +
219H ALA* 2.9 47.2 + - + +
220H LEU* 4.2 5.1 - - - +
308H ACT 3.3 28.8 + - - -
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Residues in contact with LEU 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H LYS* 3.8 11.9 - - + -
111H ILE* 3.4 44.6 - - + +
114H LEU* 3.8 23.6 - - + -
146H TYR* 3.6 29.6 - - + -
153H LEU* 3.9 2.7 - - + -
172H LEU* 3.7 25.7 - - + +
206H VAL 2.9 14.3 + - - +
207H GLU* 3.3 4.5 + - - +
209H ARG* 1.3 77.0 - - - +
211H GLN* 1.3 50.7 + - - +
213H ALA* 2.9 4.9 + - - +
214H LEU* 2.7 42.0 + - + +
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Residues in contact with GLN 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO 4.9 0.7 - - - +
184A LEU 5.9 0.2 - - - +
185A GLN* 3.5 26.5 + - + +
187A LYS* 6.3 1.1 - - - -
110H LYS* 3.8 28.2 - - + +
207H GLU* 3.0 20.7 + - + +
208H ARG* 3.9 6.5 - - - +
210H LEU* 1.3 77.5 - - - +
212H LYS* 1.3 53.1 + - + +
214H LEU* 2.9 15.2 + - - +
215H ASN* 2.7 70.3 + - - +
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Residues in contact with LYS 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS* 6.3 0.6 - - - +
208H ARG* 3.2 26.3 + - + +
209H ARG* 3.7 8.5 - - + +
211H GLN* 1.3 77.7 - - + +
213H ALA* 1.3 53.3 + - - +
215H ASN* 3.2 6.2 + - - +
217H GLN* 2.7 69.3 + - + +
218H ILE 3.7 15.0 + - - +
219H ALA* 4.3 3.8 - - - -
220H LEU 3.2 29.0 + - - +
221H LYS 4.7 8.2 + - - -
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Residues in contact with ALA 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E ILE* 4.1 6.7 - - - +
146H TYR* 3.8 40.0 - - + -
170H GLN* 4.1 17.7 - - + -
172H LEU* 4.3 0.9 - - + -
209H ARG 3.0 12.9 + - - +
210H LEU* 2.9 12.0 + - - +
212H LYS* 1.3 73.3 - - - +
214H LEU* 1.3 64.0 + - - +
215H ASN 3.0 1.8 - - - -
216H GLY* 3.0 14.9 + - - -
217H GLN 3.5 9.8 + - - -
219H ALA* 4.8 0.6 - - + +
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Residues in contact with LEU 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 4.2 43.4 - - + +
33A TYR* 5.7 0.7 - - - -
196A ASN* 4.0 6.8 + - - -
110H LYS* 4.1 26.0 - - + -
114H LEU* 4.0 12.1 - - + -
146H TYR* 3.5 34.5 - - + +
151H GLU* 5.7 0.7 - - - +
210H LEU* 2.7 42.1 + - + +
211H GLN* 2.9 24.4 + - - +
213H ALA* 1.3 73.7 - - - +
215H ASN* 1.3 59.9 - - - +
216H GLY 3.2 1.0 + - - -
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Residues in contact with ASN 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLN* 3.0 41.6 + - - +
186A TYR* 3.7 20.4 - - + +
192A SER* 4.1 8.8 - - - +
196A ASN* 2.7 26.9 + - - +
217E GLN* 5.8 0.2 + - - -
211H GLN* 2.7 39.7 + - - +
212H LYS* 3.4 8.7 - - - +
213H ALA 3.0 0.6 - - - -
214H LEU* 1.3 73.5 - - - +
216H GLY* 1.3 59.9 + - - +
217H GLN* 2.7 32.1 + - - +
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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