Contacts of the helix formed by residues 212 - 225 (chain A) in PDB entry 2XMS
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 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLY 3.2 27.6 + - - +
91A MET* 3.5 30.3 + - - +
95A ALA* 5.3 7.8 - - + +
97A VAL* 5.0 5.8 - - + -
210A ALA* 3.5 15.9 - - - +
211A PRO* 1.3 84.1 - - + +
213A LEU* 1.3 57.2 + - - +
214A ASP 3.2 3.6 - - - -
215A ASN* 2.9 28.7 + - + +
216A ILE* 2.9 17.2 + - - +
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Residues in contact with LEU 213 (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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179A ILE* 4.6 13.9 - - + -
180A PRO* 3.8 31.9 - - + -
183A ILE* 5.0 0.2 - - + -
207A ILE* 3.7 21.1 - - + +
208A THR 4.2 13.5 - - - +
210A ALA* 3.5 16.4 + - + +
211A PRO 3.4 3.8 + - - -
212A ASN* 1.3 77.0 + - - +
214A ASP* 1.3 60.4 + - - +
216A ILE* 3.2 25.5 + - + +
217A GLU* 2.9 30.4 + - + +
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Residues in contact with ASP 214 (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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97A VAL* 3.8 28.5 - - + +
98A PHE 5.7 0.7 - - - +
211A PRO 5.2 0.6 + - - +
212A ASN 3.2 0.6 - - - -
213A LEU* 1.3 81.8 - - - +
215A ASN* 1.3 60.9 + - - +
217A GLU* 3.5 14.8 + - - +
218A LEU* 3.4 26.8 + - - +
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Residues in contact with ASN 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLY* 3.1 36.6 + - - +
91A MET* 3.4 15.2 - - + +
95A ALA* 4.2 1.8 - - - +
96A PRO 2.8 26.2 + - - -
97A VAL* 3.6 6.3 - - - +
98A PHE* 3.0 38.0 + - + +
104A TYR* 4.6 1.4 - - - -
212A ASN* 2.9 17.2 + - - +
214A ASP* 1.3 76.6 - - - +
216A ILE* 1.3 64.9 + - - +
218A LEU* 3.1 19.5 + - - +
219A TYR 3.3 9.5 + - - -
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Residues in contact with ILE 216 (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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57A VAL* 4.1 0.9 - - + +
58A GLY* 3.6 40.2 - - - +
59A LEU 5.8 0.2 - - - +
91A MET* 3.8 23.8 - - - -
183A ILE* 3.4 26.5 - - + -
206A ILE* 6.5 0.2 - - + -
207A ILE* 5.1 3.8 - - + +
210A ALA* 3.7 20.4 - - + -
212A ASN* 2.9 31.4 + - - +
213A LEU* 3.5 17.9 - - + +
215A ASN* 1.3 74.3 - - - +
217A GLU* 1.3 57.3 + - - +
219A TYR* 3.2 4.9 + - - +
220A TRP* 2.9 25.6 + - - +
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Residues in contact with GLU 217 (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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179A ILE* 3.2 48.3 - - + +
213A LEU* 2.9 17.3 + - - +
214A ASP* 3.7 16.6 - - - +
215A ASN 3.2 0.4 - - - -
216A ILE* 1.3 78.2 - - - +
218A LEU* 1.3 60.2 + - + +
220A TRP* 3.3 9.4 + - + +
221A ASN* 2.9 43.3 + - - +
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Residues in contact with LEU 218 (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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98A PHE* 4.1 28.7 - - + +
99A PRO 5.5 0.9 - - - +
102A TYR* 4.3 21.5 - - + +
104A TYR* 3.7 40.9 - - + +
214A ASP 3.4 16.6 + - - +
215A ASN* 3.1 8.6 + - - +
217A GLU* 1.3 81.0 - - + +
219A TYR* 1.3 55.8 + - - +
221A ASN* 3.4 15.2 + - - +
222A SER* 3.0 27.0 + - - -
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Residues in contact with TYR 219 (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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54A TYR* 3.6 11.7 - + - -
55A HIS* 2.9 35.8 + + - -
56A ASP 3.7 19.7 - - - -
57A VAL* 3.7 17.9 - - + -
58A GLY 4.6 2.9 - - - -
88A ALA* 3.9 14.4 - - + -
91A MET* 3.9 16.6 - - + -
104A TYR* 3.7 23.7 - + - +
107A LEU* 4.0 6.3 - - + -
110A LEU* 3.8 30.3 - - + -
133A ALA* 3.5 27.9 - - + +
134A GLY 3.7 2.3 + - - -
137A ILE* 3.8 1.8 - - + +
215A ASN 3.3 1.6 + - - -
216A ILE 3.2 7.7 + - - +
218A LEU* 1.3 73.5 - - - +
220A TRP* 1.3 59.8 + - - +
222A SER* 3.3 4.7 - - - -
223A TYR* 2.9 26.9 + - - +
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Residues in contact with TRP 220 (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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57A VAL* 3.6 25.0 - - + +
162A LYS* 5.8 0.7 - - - -
170A HIS* 3.7 20.6 + + - -
179A ILE* 4.7 18.3 - - + +
182A MET* 3.8 31.3 - - + +
183A ILE* 3.8 22.3 - - + +
186A HIS* 3.6 39.5 - + + -
216A ILE 2.9 12.9 + - - +
217A GLU* 3.3 11.9 - - + +
219A TYR* 1.3 76.5 - - - +
221A ASN* 1.3 67.1 + - - +
223A TYR* 3.2 15.4 + + - +
224A ASN* 2.9 65.7 + - - +
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Residues in contact with ASN 221 (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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179A ILE* 6.2 0.2 - - - +
217A GLU* 2.9 32.5 + - - +
218A LEU* 3.5 17.0 - - - +
219A TYR 3.3 0.2 - - - -
220A TRP* 1.3 87.1 - - - +
222A SER* 1.3 63.7 + - - +
224A ASN* 3.2 8.3 + - - +
225A ASN* 2.9 40.5 + - - +
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Residues in contact with SER 222 (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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104A TYR* 3.9 7.2 + - - +
105A PRO 2.5 29.9 + - - -
106A SER* 3.4 9.9 - - - +
107A LEU* 3.7 26.4 + - - +
218A LEU 3.0 9.7 + - - -
219A TYR* 3.3 13.9 - - - -
221A ASN* 1.3 71.7 - - - +
223A TYR* 1.3 67.3 + - - +
225A ASN* 3.3 5.2 + - - +
226A ARG* 3.2 15.6 + - - -
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Residues in contact with TYR 223 (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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57A VAL* 3.9 14.4 - - + -
107A LEU* 3.9 9.7 - - + +
132A GLY 4.6 3.3 - - - -
133A ALA* 3.6 33.2 - - + -
136A TYR* 5.4 2.0 - - + -
156A ASN 5.2 1.2 + - - -
158A ASP* 3.7 18.3 + - + +
162A LYS* 5.5 2.9 - - - -
186A HIS* 3.6 31.3 - + - -
219A TYR 2.9 15.5 + - - +
220A TRP* 3.2 18.6 + + - +
222A SER* 1.3 72.5 - - - +
224A ASN* 1.3 80.4 + - - +
226A ARG* 3.0 73.4 + - - +
253A HIS* 3.7 10.0 - + - -
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Residues in contact with ASN 224 (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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162A LYS* 3.4 36.6 + - - +
167A TRP* 3.4 32.4 - - + -
170A HIS* 3.5 14.8 + - - -
220A TRP* 2.9 56.2 + - - +
221A ASN* 3.2 11.5 + - - +
223A TYR* 1.3 93.0 - - - +
225A ASN* 1.3 61.2 + - - +
226A ARG* 3.6 5.5 + - - +
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Residues in contact with ASN 225 (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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167A TRP* 3.4 25.4 - - - -
221A ASN* 2.9 36.5 + - - +
222A SER* 3.7 5.6 - - - +
223A TYR 3.1 0.4 - - - -
224A ASN* 1.3 80.5 - - - +
226A ARG* 1.3 65.3 + - - +
227A ARG* 3.7 1.4 + - - +
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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