Contacts of the helix formed by residues 192 - 211 (chain A) in PDB entry 1P4D
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 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LEU* 4.0 15.4 - - - +
188A ASN* 2.8 25.8 + - - +
189A VAL 3.2 4.1 + - - -
190A TYR 2.8 1.0 - - - -
191A ALA* 1.3 87.1 - - - +
193A GLN* 1.3 64.8 + - - +
194A ILE* 3.3 2.5 - - - -
195A ALA* 3.0 26.8 + - + +
196A PHE* 3.0 35.7 + - + -
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Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A MET* 2.8 38.7 + - + +
3A SER* 3.5 14.1 - - - +
4A ILE* 3.7 24.9 - - + +
189A VAL 2.9 11.5 + - - +
190A TYR* 2.9 27.4 + - - +
191A ALA 3.6 0.4 - - - -
192A ASN* 1.3 76.7 - - - +
194A ILE* 1.3 71.8 + - + +
196A PHE* 3.4 2.1 + - - +
197A GLY* 3.1 19.4 + - - -
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Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ASN 3.3 1.0 - - - -
193A GLN* 1.3 87.5 - - + +
195A ALA* 1.3 54.4 + - - +
197A GLY* 3.1 3.1 + - - -
198A ARG* 2.7 46.8 + - + +
201A ARG* 4.2 2.3 + - - +
221A HIS* 4.0 44.0 - - + +
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ASN* 3.0 26.6 + - + +
194A ILE* 1.3 83.9 - - + +
196A PHE* 1.3 59.1 + - + +
198A ARG* 3.2 7.1 + - - +
199A LEU* 2.8 38.3 + - + +
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Residues in contact with PHE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A MET* 3.6 37.5 - - + -
84A PHE* 4.3 3.0 - - + -
113A ALA* 4.2 8.8 - - + +
116A GLN* 4.0 10.8 - - + -
117A VAL* 3.8 38.8 - - + -
120A LEU* 3.7 29.4 - - + -
189A VAL* 4.1 14.1 - - + -
192A ASN* 3.0 44.8 + - + +
195A ALA* 1.3 77.1 - - + +
197A GLY* 1.3 63.9 + - - +
199A LEU* 3.2 20.4 + - + +
200A TYR* 3.0 24.3 + - - +
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Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.2 3.1 - - - -
2A MET* 4.1 22.6 - - - +
193A GLN 3.1 15.0 + - - -
194A ILE* 3.5 3.1 - - - -
196A PHE* 1.3 79.7 - - - +
198A ARG* 1.3 56.4 + - - +
200A TYR* 3.3 4.2 + - - +
201A ARG* 2.8 46.4 + - - +
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Residues in contact with ARG 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ILE* 2.7 36.1 + - + +
195A ALA* 3.7 7.4 - - - +
197A GLY* 1.3 71.9 - - - +
199A LEU* 1.3 58.5 + - - +
201A ARG* 3.0 20.9 - - - +
202A GLU* 2.8 53.2 + - + +
221A HIS* 2.7 52.9 + - + +
222A GLY* 3.7 11.1 - - - +
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 4.1 28.3 - - + -
113A ALA* 4.6 6.5 - - + -
116A GLN* 3.8 27.4 - - + -
195A ALA* 2.8 22.7 + - + +
196A PHE* 3.2 27.6 + - + +
198A ARG* 1.3 76.6 - - + +
200A TYR* 1.3 64.7 + - - +
202A GLU* 4.0 3.8 - - - +
203A LYS* 3.1 24.6 + - - +
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Residues in contact with TYR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 4.5 10.5 - - - -
84A PHE* 3.6 35.2 - + + -
85A SER 3.3 22.0 - - - -
86A ALA* 3.2 18.7 - - - +
87A PRO* 5.0 2.0 - - + -
106A HIS* 2.8 37.4 - + - -
109A ALA* 3.4 42.0 - - + +
110A VAL* 3.8 9.9 - - + -
113A ALA* 4.0 4.4 - - + +
196A PHE 3.0 12.5 + - - +
197A GLY 3.7 4.5 - - - +
199A LEU* 1.3 75.7 - - - +
201A ARG* 1.3 84.0 + - + +
203A LYS* 3.1 4.2 + - - +
204A LEU* 3.0 38.8 + - + +
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 2.9 46.0 - - - +
194A ILE* 4.2 2.4 + - - +
197A GLY* 2.8 21.2 + - - +
198A ARG* 3.0 50.6 - - - +
200A TYR* 1.3 86.1 - - + +
202A GLU* 1.3 61.6 + - - +
204A LEU* 3.6 3.7 + - - +
205A LYS 3.3 10.4 + - - -
221A HIS* 3.3 22.9 + - - +
222A GLY 3.5 14.4 - - - +
223A MET* 3.9 24.0 - - - +
224A TRP* 3.1 39.3 + - + +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ARG* 2.8 41.3 + - - +
199A LEU* 4.0 3.8 - - - +
201A ARG* 1.3 73.8 - - - +
203A LYS* 1.3 63.3 + - - +
205A LYS* 3.6 36.8 + - - +
206A GLU* 3.4 30.9 + - - +
222A GLY* 5.3 4.5 - - - +
224A TRP* 5.3 0.7 - - - -
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Residues in contact with LYS 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLN* 4.3 6.3 - - - +
109A ALA* 3.8 23.8 - - + +
112A PHE* 3.8 41.8 - - + -
199A LEU 3.1 16.6 + - - +
200A TYR 3.1 4.6 + - - +
202A GLU* 1.3 73.5 - - - +
204A LEU* 1.3 65.0 + - - +
206A GLU* 3.4 27.8 + - - +
207A GLN* 3.2 47.0 + - + +
206B GLU* 5.9 0.6 + - - -
207B GLN* 6.3 1.2 - - - +
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA* 4.3 4.7 - - + -
87A PRO* 3.6 26.9 - - + -
90A VAL* 4.5 6.7 - - + -
102A LEU 4.8 1.8 - - - +
105A ALA* 3.7 13.9 - - + -
106A HIS* 3.6 34.3 - - + +
109A ALA* 3.9 7.8 - - + +
200A TYR* 3.0 39.5 + - + +
201A ARG* 3.7 5.6 - - - +
203A LYS* 1.3 76.7 - - - +
205A LYS* 1.3 57.4 + - - +
207A GLN* 3.1 4.8 + - - +
208A VAL* 2.8 41.4 + - + +
224A TRP* 3.9 12.8 - - + -
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ARG 3.3 4.4 + - - +
202A GLU* 3.6 35.4 + - - +
203A LYS 3.3 0.2 - - - -
204A LEU* 1.3 80.2 - - - +
206A GLU* 1.3 58.6 + - + +
208A VAL* 4.4 1.1 - - - -
209A GLU* 2.9 42.9 + - - +
215A THR* 3.0 34.7 + - + +
217A VAL* 5.0 12.1 - - - +
222A GLY 5.1 2.2 + - - -
224A TRP* 3.5 48.6 - - + +
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLU* 3.4 22.8 + - - +
203A LYS* 3.6 31.5 + - - +
204A LEU 3.2 0.6 - - - -
205A LYS* 1.3 80.3 - - + +
207A GLN* 1.3 70.3 + - - +
209A GLU* 3.5 5.4 + - - +
210A ALA* 3.0 22.3 + - - +
605B EDO 4.1 8.3 + - - +
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Residues in contact with GLN 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ALA* 3.6 25.4 - - + +
108A GLN* 2.4 34.7 + - + +
203A LYS* 3.2 35.4 + - + +
204A LEU 3.1 4.6 + - - +
206A GLU* 1.3 80.2 - - - +
208A VAL* 1.3 56.8 + - - +
210A ALA* 2.8 30.0 + - - +
211A LEU* 3.1 7.9 + - - +
600A EDO 3.1 29.4 + - - -
108B GLN* 4.5 3.6 + - - -
203B LYS* 6.1 0.2 - - - +
605B EDO 2.6 28.7 + - - -
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 4.6 4.5 - - + -
102A LEU* 3.7 21.1 - - + -
105A ALA* 4.5 1.8 - - + -
204A LEU* 2.8 44.7 + - + +
205A LYS 4.0 2.7 - - - +
207A GLN* 1.3 72.3 - - - +
209A GLU* 1.3 61.6 + - - +
211A LEU* 3.1 24.7 + - - +
213A TYR* 3.5 33.0 + - + +
215A THR* 4.2 11.7 - - + -
224A TRP* 4.1 20.2 - - + -
226A MET* 4.5 8.1 - - - -
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LYS* 2.9 35.5 + - - +
206A GLU* 4.0 4.8 - - - +
208A VAL* 1.3 77.0 - - - +
210A ALA* 1.3 62.6 + - - +
212A GLY* 3.1 9.7 + - - -
213A TYR 3.4 17.7 - - - +
214A GLU* 5.1 0.4 - - - -
215A THR* 2.5 37.9 + - + +
302A ARG* 3.5 21.4 + - - +
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Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A GLU 3.0 13.4 + - - +
207A GLN* 2.8 14.4 + - - +
209A GLU* 1.3 72.4 - - - +
211A LEU* 1.3 60.7 + - - +
212A GLY* 3.1 6.2 + - - -
299A ALA* 4.5 7.4 - - - +
600A EDO 4.3 3.6 - - - +
112B PHE* 5.7 1.8 - - + -
115B ARG* 4.4 12.7 + - - +
116B GLN* 5.9 1.6 + - - -
605B EDO 4.1 30.5 - - - +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP* 4.4 1.3 - - - +
101A ARG* 2.9 74.0 + - + +
102A LEU* 3.8 28.3 - - + -
105A ALA* 5.1 1.3 - - + -
207A GLN 3.1 16.7 + - - +
208A VAL* 3.1 9.3 + - - +
210A ALA* 1.3 77.1 - - - +
212A GLY* 1.3 58.6 + - - +
213A TYR* 3.6 8.3 - - + -
295A ALA* 3.4 12.6 - - - +
296A ASP* 4.6 1.7 - - - +
299A ALA* 3.6 7.7 - - - +
600A EDO 3.7 14.6 - - - +
36B ARG* 5.4 1.2 + - - -
115B ARG* 3.6 25.4 - - - +
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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