Contacts of the helix formed by residues 130 - 138 (chain A) in PDB entry 2Q4E
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 MSE 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.5 9.4 - - + -
20A LYS* 3.2 42.4 - - + -
21A VAL* 3.9 27.8 - - + -
101A GLU* 4.7 8.5 - - - +
102A LYS* 5.0 0.8 - - - +
128A GLY 3.2 11.7 - - - +
129A THR* 1.3 68.7 - - - +
131A TRP* 1.3 55.2 + - - +
132A VAL 3.1 2.7 - - - -
133A HIS* 2.8 37.9 + - - +
134A ASN 4.0 1.2 + - - -
191A TYR* 5.0 8.8 - - + +
267A ILE* 4.4 8.1 - - + -
306A GLN* 4.0 18.9 - - + +
307A GLU* 4.1 11.0 - - + -
310A MSE 4.0 28.9 - - + -
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Residues in contact with TRP 131 (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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129A THR* 3.7 24.1 - - + +
130A MSE 1.3 77.2 - - - +
132A VAL* 1.3 65.7 - - + +
133A HIS 2.9 2.6 + - - -
134A ASN* 3.1 12.3 + - + +
137A THR* 2.8 35.4 + - + -
140A LEU* 6.0 2.9 - - + -
191A TYR* 3.7 21.8 + + - -
194A ARG* 3.6 22.1 - - + +
195A ALA* 3.9 20.9 - - + -
198A LEU* 3.6 33.9 - - + -
251A ILE* 4.8 5.2 - - + -
265A PHE* 2.8 61.7 - + + +
266A ILE* 4.3 8.7 - - + -
306A GLN* 3.8 19.6 - - - +
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Residues in contact with VAL 132 (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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129A THR* 3.6 14.1 - - + +
130A MSE 2.9 3.6 + - - -
131A TRP* 1.3 109.3 - - + +
133A HIS* 1.3 84.3 + - + +
134A ASN 4.4 0.3 - - - +
137A THR* 3.7 20.4 - - + +
194A ARG* 3.7 32.3 - - + +
198A LEU* 4.8 5.2 - - + -
202A PHE* 5.6 3.4 - - + -
331A TYR* 6.2 0.4 - - - +
332A TRP* 4.3 13.2 - - + -
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Residues in contact with HIS 133 (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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126A MSE 3.7 31.9 - - + -
127A ASP* 5.5 0.7 - - - -
129A THR 3.8 9.1 + - - -
130A MSE 2.8 15.5 + - - +
132A VAL* 1.3 86.7 - - + +
134A ASN* 1.3 65.7 + - - +
135A PRO* 3.5 2.8 - - - +
306A GLN* 4.1 5.6 - - - +
309A CYS* 3.8 17.2 - - - +
310A MSE 3.8 31.8 - - + +
313A GLU* 4.2 17.2 - - + +
332A TRP* 3.0 44.1 - + - -
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Residues in contact with ASN 134 (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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130A MSE 4.0 1.6 + - - -
131A TRP* 3.1 14.7 + - + +
132A VAL 4.4 0.2 - - - +
133A HIS* 1.3 79.7 - - - +
135A PRO* 1.3 77.2 - - - +
136A ARG* 2.8 41.8 + - + +
137A THR* 2.9 22.7 + - - +
138A ALA* 4.1 1.0 + - - +
268A PRO* 4.0 18.4 - - - +
271A GLU 5.5 1.0 + - - -
274A ALA* 3.9 6.1 - - - +
302A THR* 3.4 17.8 + - - +
306A GLN* 3.3 37.8 + - + +
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Residues in contact with PRO 135 (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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133A HIS 3.5 5.4 - - - +
134A ASN* 1.3 91.4 - - - +
136A ARG* 1.3 52.7 + - - +
138A ALA* 2.7 32.4 + - + +
139A LEU* 2.9 15.4 - - + +
300A VAL* 4.4 8.3 - - + -
301A LYS 4.4 7.4 - - - +
302A THR* 3.4 33.0 - - + -
304A LEU 4.9 0.4 - - - +
306A GLN* 5.6 0.2 - - - -
309A CYS* 4.3 18.6 - - - -
312A ARG* 6.2 0.9 - - - +
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Residues in contact with ARG 136 (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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134A ASN* 2.8 24.5 + - - +
135A PRO* 1.3 72.9 - - - +
137A THR* 1.3 63.6 + - - +
138A ALA 3.2 0.9 + - - -
139A LEU* 3.3 9.7 - - - +
140A LEU* 3.3 24.7 - - + +
262A VAL* 4.3 4.4 - - - +
264A ASP* 2.4 33.6 + - - -
265A PHE* 3.3 35.0 + - - +
268A PRO* 3.7 20.6 - - - +
274A ALA* 3.6 24.0 - - + +
275A SER 2.8 38.1 + - - +
276A PHE* 3.6 24.9 - - + -
300A VAL* 3.6 16.3 - - + +
306A GLN* 5.2 0.6 + - - -
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Residues in contact with THR 137 (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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131A TRP* 2.8 36.0 + - + -
132A VAL* 3.7 20.2 - - - +
134A ASN* 2.9 15.1 + - - +
136A ARG* 1.3 81.6 + - - +
138A ALA* 1.3 56.2 - - - +
140A LEU* 4.6 7.5 - - + +
141A LYS* 3.0 29.6 + - + +
198A LEU* 3.3 32.1 - - + -
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Residues in contact with ALA 138 (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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134A ASN 4.1 0.6 + - - +
135A PRO* 2.7 16.9 + - + +
137A THR* 1.3 75.9 - - - +
139A LEU* 1.3 60.0 + - + +
140A LEU 2.9 11.3 + - - -
141A LYS* 3.2 14.9 + - - +
142A GLU* 2.8 35.6 + - - +
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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