Contacts of the helix formed by residues 211 - 225 (chain A) in PDB entry 5M64
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 THR 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ILE* 5.6 3.4 - - + +
209A THR* 3.2 17.7 - - - +
210A ALA* 1.3 78.9 - - - +
212A VAL* 1.3 72.1 + - + +
213A ASN* 3.2 2.9 - - - -
214A ASP* 3.1 9.9 + - - +
215A GLU* 3.1 28.2 + - - +
1592A GLN* 4.9 3.6 - - - -
173E SER* 3.5 24.0 - - - +
177E ARG* 3.7 17.6 + - - -
215E MET* 3.5 35.2 - - + -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.6 17.2 - - + +
126A GLN 5.6 0.9 - - - +
127A TYR 4.6 15.7 - - - +
128A GLY* 5.2 7.2 - - - -
129A LEU 5.9 0.2 - - - +
130A ILE* 5.6 8.3 - - + +
207A SER 4.7 5.4 - - - +
208A PHE* 3.7 21.3 - - + -
209A THR* 3.4 40.2 - - - +
211A THR* 1.3 81.9 - - + +
213A ASN* 1.3 60.6 + - - +
215A GLU* 3.4 9.1 + - + +
216A ARG* 3.0 37.1 + - + +
173E SER* 5.2 5.2 - - - +
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Residues in contact with ASN 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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208A PHE* 3.6 22.4 - - + -
209A THR 3.6 14.4 + - - -
210A ALA* 3.0 24.4 - - - +
212A VAL* 1.3 74.2 - - - +
214A ASP* 1.3 65.1 + - - -
216A ARG* 4.0 7.8 - - - +
217A LYS* 2.8 54.7 + - - +
1605A THR* 3.2 19.4 - - - +
1606A SER 3.0 30.9 + - - +
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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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210A ALA 3.2 8.7 - - - +
211A THR* 3.1 10.1 + - - +
213A ASN* 1.3 83.2 + - - +
215A GLU* 1.3 59.8 + - + +
217A LYS* 3.9 4.1 - - - +
218A LYS* 2.9 30.7 + - - +
1592A GLN* 3.0 28.3 - - - +
1604A GLU* 4.2 6.4 - - - +
1605A THR* 2.2 34.2 + - - +
177E ARG* 3.7 20.8 + - - +
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS* 6.2 0.3 - - - -
125A LEU* 4.1 15.5 - - + -
130A ILE* 3.7 30.7 - - + +
134A TYR* 4.1 17.9 + - - -
211A THR* 3.1 18.4 + - - +
212A VAL* 3.8 8.5 - - - +
214A ASP* 1.3 78.8 - - - +
216A ARG* 1.3 56.7 + - - +
218A LYS* 3.3 8.7 + - - +
219A LEU* 2.9 43.4 + - + +
177E ARG* 4.0 18.5 + - - -
192E ARG* 4.6 9.3 + - - -
215E MET* 5.5 0.7 - - - +
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Residues in contact with ARG 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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122A LEU* 5.6 7.1 - - + +
125A LEU* 3.7 24.7 - - + -
126A GLN* 5.5 0.9 - - - +
208A PHE* 5.1 8.9 - - - -
212A VAL* 3.0 25.0 + - - +
213A ASN* 4.0 6.8 - - - +
215A GLU* 1.3 76.3 - - - +
217A LYS* 1.3 63.1 + - - +
219A LEU* 3.3 6.6 + - - +
220A VAL* 2.9 31.5 + - - +
337A TYR* 3.5 34.4 + - + +
338A VAL* 4.8 3.2 + - - +
340A HIS 3.1 14.5 + - - -
341A SER* 4.0 16.8 + - - +
1628A ASP* 2.8 43.7 + - - -
1630A GLU* 5.5 0.2 - - - +
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Residues in contact with LYS 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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208A PHE* 5.8 0.8 - - - -
213A ASN* 2.8 40.0 + - - +
214A ASP* 4.0 3.4 - - - +
216A ARG* 1.3 83.0 - - + +
218A LYS* 1.3 57.8 + - - +
220A VAL* 3.2 9.9 - - + +
221A HIS* 2.9 49.5 + - + +
1604A GLU* 3.7 40.6 + - + +
1605A THR* 4.5 8.2 - - - +
1606A SER 5.4 2.6 + - - +
1612A LYS* 5.6 2.7 - - - +
1624A LYS* 4.9 23.3 - - + +
1630A GLU* 5.9 0.8 + - - -
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 5.0 10.8 + - - +
214A ASP 2.9 19.4 + - - +
215A GLU* 3.7 11.0 - - - +
217A LYS* 1.3 76.6 - - - +
219A LEU* 1.3 71.3 + - + +
221A HIS* 3.6 6.8 + - + +
222A GLU* 3.0 43.7 + - - +
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Residues in contact with LEU 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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118A TYR* 4.5 11.4 - - + -
121A LYS* 4.3 25.6 - - + -
122A LEU* 3.8 25.8 - - + -
125A LEU* 5.0 5.2 - - + -
134A TYR* 6.1 2.2 - - + +
215A GLU* 2.9 32.7 + - - +
216A ARG* 3.7 7.0 - - - +
217A LYS 3.3 0.2 - - - -
218A LYS* 1.3 91.0 - - + +
220A VAL* 1.3 60.5 + - - +
222A GLU* 3.1 22.4 + - - +
223A PHE* 2.9 56.9 + - + -
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Residues in contact with VAL 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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97A TYR* 5.4 2.9 - - - +
122A LEU* 6.4 0.2 - - + -
216A ARG 2.9 17.9 + - - +
217A LYS* 3.2 21.3 - - + +
219A LEU* 1.3 73.9 - - - +
221A HIS* 1.3 68.0 + - + +
223A PHE* 3.2 18.7 + - + +
224A HIS* 2.4 57.0 + - + -
338A VAL* 5.1 13.2 - - + +
1624A LYS* 5.4 8.5 - - + +
1627A LEU* 6.1 4.9 - - + -
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Residues in contact with HIS 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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217A LYS* 2.9 38.5 + - + +
218A LYS* 3.8 7.2 - - - +
220A VAL* 1.3 86.1 - - + +
222A GLU* 1.3 60.0 + - - +
224A HIS* 3.2 12.3 + + + +
225A LYS* 3.0 42.6 + - + +
1604A GLU* 6.2 3.6 - - + -
1624A LYS* 4.2 19.7 + - - -
58S A 4.6 18.3 + - - -
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Residues in contact with GLU 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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118A TYR* 3.3 28.7 + - - -
218A LYS* 3.0 34.5 + - + +
219A LEU* 3.1 29.0 + - - +
221A HIS* 1.3 75.5 - - - +
223A PHE* 1.3 59.8 + - + +
225A LYS* 3.2 8.6 + - + +
226A LYS* 3.0 37.8 + - + +
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Residues in contact with PHE 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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96A ILE* 4.7 5.2 - - + +
118A TYR* 3.4 54.1 - + + -
122A LEU* 3.7 28.5 - - + -
219A LEU* 2.9 42.7 + - + -
220A VAL* 3.2 22.6 + - + +
222A GLU* 1.3 80.3 - - + +
224A HIS* 1.3 60.9 + - + +
226A LYS* 3.2 23.2 + - + +
228A LEU* 3.8 10.6 - - - +
334A VAL* 6.4 2.2 - - + -
338A VAL* 4.7 14.1 - - + -
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Residues in contact with HIS 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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93A GLN* 4.3 19.3 + - - -
96A ILE* 3.5 47.6 - - + +
97A TYR* 5.6 7.1 - + - -
99A ARG* 5.7 0.3 + - - -
220A VAL* 2.4 51.4 + - + +
221A HIS* 3.6 15.7 - + - +
222A GLU 3.2 0.6 - - - -
223A PHE* 1.3 80.0 - - + +
225A LYS* 1.3 67.3 + - + +
226A LYS 3.2 4.8 + - - -
228A LEU* 4.3 16.5 - - - +
1624A LYS* 5.6 3.9 + - - -
1627A LEU* 6.1 1.8 - - + -
59S G 5.1 10.4 + - - +
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Residues in contact with LYS 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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221A HIS* 3.0 30.9 + - + +
222A GLU* 3.2 11.9 + - + +
224A HIS* 1.3 84.0 - - - +
226A LYS* 1.3 64.5 + - - +
229A SER* 5.4 5.6 - - - -
58S A 3.5 32.5 + - - +
59S G 4.7 12.4 + - - +
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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