Contacts of the helix formed by residues 202 - 212 (chain A) in PDB entry 4D87
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 GLN 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ASP* 3.7 25.1 + - - -
193A GLN* 4.9 1.8 - - - +
196A GLY* 2.7 33.2 + - - +
198A ILE* 3.1 25.8 - - + +
199A ASN* 3.7 17.1 - - - +
201A PRO* 1.3 81.7 + - - +
203A LEU* 1.3 79.9 + - + +
204A HIS 2.8 4.5 + - - -
205A ASN* 3.1 6.1 + - - +
206A ARG* 3.5 18.8 + - - +
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Residues in contact with LEU 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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94A TRP* 3.9 16.8 - - + -
163A PRO* 3.8 27.8 - - + +
167A ASP* 4.3 11.4 - - + +
168A VAL* 4.1 24.0 - - + +
171A ALA* 4.0 22.2 - - + -
193A GLN* 3.6 22.0 - - + +
194A LEU* 3.6 23.8 - - + +
202A GLN* 1.3 78.9 - - + +
204A HIS* 1.3 55.5 + - - +
206A ARG* 2.8 9.5 + - - +
207A VAL* 2.6 41.6 + - - +
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Residues in contact with HIS 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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60A HIS* 5.3 8.3 - + - -
65A PHE* 3.0 42.6 - + + -
94A TRP* 4.9 2.1 - - - -
194A LEU* 3.1 21.2 + - + +
195A GLU* 3.2 6.0 + - + +
202A GLN 2.8 3.0 + - - -
203A LEU* 1.3 79.2 - - - +
205A ASN* 1.3 86.1 + - - +
207A VAL* 3.4 3.0 + - - +
208A HIS* 3.0 50.8 + + - -
230A HIS* 2.9 39.5 - + + +
231A HIS* 3.4 13.7 - + - -
234A VAL* 4.2 10.5 - - + -
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Residues in contact with ASN 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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60A HIS* 6.3 0.4 - - - +
195A GLU* 2.7 41.6 + - - +
196A GLY* 3.5 5.3 - - - +
197A PHE* 3.3 35.7 - - - -
201A PRO* 4.1 15.7 - - + -
202A GLN 3.1 4.9 + - - +
204A HIS* 1.3 91.8 + - - +
206A ARG* 1.3 61.3 + - - +
208A HIS* 3.2 15.4 + - - +
209A ARG* 3.3 19.6 + - + +
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Residues in contact with ARG 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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158A GLU 4.0 12.1 + - - -
159A ALA* 3.7 22.3 - - + +
160A PRO* 3.9 6.5 - - - +
161A THR* 2.4 67.6 + - - +
162A LEU* 4.2 1.7 + - - -
163A PRO* 4.0 17.0 - - - -
201A PRO* 3.3 32.1 + - - +
202A GLN* 3.2 24.1 + - - +
203A LEU 2.8 10.9 + - - +
205A ASN* 1.3 74.3 - - - +
207A VAL* 1.3 69.6 + - - +
209A ARG 3.6 0.3 + - - -
210A TRP* 3.1 19.5 + - - +
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Residues in contact with VAL 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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92A TRP* 3.4 31.0 - - + -
94A TRP* 3.4 29.8 - - + -
162A LEU* 3.5 16.1 - - + +
163A PRO* 4.0 2.9 - - + +
203A LEU 2.6 26.0 + - - +
204A HIS 3.6 1.3 - - - +
206A ARG* 1.3 71.2 - - - +
208A HIS* 1.3 56.9 + - - +
210A TRP* 3.0 23.6 + - - +
211A VAL* 3.2 10.0 + - + +
215A MET* 5.6 1.6 - - - -
230A HIS* 3.3 41.5 - - + +
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Residues in contact with HIS 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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42A HIS* 6.0 1.2 - + - -
60A HIS* 6.1 1.8 - + - -
204A HIS* 3.0 53.0 + + - -
205A ASN* 3.2 11.2 + - - +
207A VAL* 1.3 76.5 - - - +
209A ARG* 1.3 63.8 + - + +
211A VAL 3.7 0.5 + - - -
212A GLY 3.4 10.4 + - - -
215A MET* 2.8 73.5 + - + +
216A GLY* 3.4 3.8 - - - -
221A ALA* 4.2 7.6 - - + +
227A PHE* 3.8 22.2 - + - -
230A HIS* 3.6 10.3 + + - -
231A HIS* 3.8 3.2 + - - -
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Residues in contact with ARG 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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152A ASN 4.9 0.9 - - - +
154A GLY 4.9 1.0 + - - -
155A ALA 5.3 0.2 + - - -
156A THR* 2.8 35.2 + - + +
158A GLU* 2.1 52.9 + - - +
159A ALA* 3.9 14.8 - - + +
201A PRO* 4.5 11.9 - - + +
205A ASN* 3.3 17.0 + - + +
208A HIS* 1.3 76.5 - - + +
210A TRP* 1.3 66.8 + - - +
212A GLY* 3.5 10.6 + - - +
216A GLY* 4.5 17.7 - - - +
402A SDS 2.3 47.1 + - - +
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Residues in contact with TRP 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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92A TRP* 4.8 0.4 - + - -
103A PRO* 4.2 38.5 - - + +
104A SER* 4.7 1.8 - - - -
109A TRP* 4.1 13.0 - + - -
152A ASN 3.3 1.7 - - - +
153A PHE* 3.2 51.3 - + + -
154A GLY* 2.5 34.8 + - - -
159A ALA* 3.7 12.7 - - - +
160A PRO 3.7 6.8 + - - -
161A THR* 3.3 19.7 - - - +
162A LEU* 3.1 57.5 - - + +
206A ARG 3.1 14.8 + - - +
207A VAL 3.0 11.8 + - - +
209A ARG* 1.3 78.5 - - - +
211A VAL* 1.3 73.8 + - + +
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Residues in contact with VAL 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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92A TRP* 4.0 18.8 - - + -
109A TRP* 4.4 6.7 - - + -
151A ARG* 3.4 26.9 - - + -
152A ASN 2.9 24.2 + - - -
153A PHE* 3.6 11.4 - - + -
207A VAL 3.2 13.3 + - - +
208A HIS 3.7 0.6 + - - +
209A ARG 3.4 0.2 - - - -
210A TRP* 1.3 92.4 - - + +
212A GLY* 1.3 63.7 + - - +
215A MET* 3.8 32.8 - - + -
224A ASP* 4.2 5.6 - - - +
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Residues in contact with GLY 212 (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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150A LYS 3.9 4.0 - - - +
152A ASN* 4.1 10.3 - - - -
208A HIS 3.4 10.3 + - - -
209A ARG 3.5 9.3 + - - -
210A TRP 3.3 3.0 - - - -
211A VAL* 1.3 86.3 - - - +
213A GLY* 1.3 70.0 + - - +
214A GLN 3.4 0.2 + - - -
215A MET* 3.1 17.2 + - - +
216A GLY* 3.9 5.6 - - - -
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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