Contacts of the strand formed by residues 136 - 144 (chain D) in PDB entry 3QUM
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 SER 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D GLY* 3.0 7.2 - - - +
135D SER* 1.3 82.0 + - - +
137D VAL* 1.3 63.4 + - - +
138D THR* 4.4 7.0 - - - +
183D THR* 5.0 10.4 + - - +
184D VAL* 3.3 16.5 + - - -
185D THR* 4.3 1.6 + - - -
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Residues in contact with VAL 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D PRO* 3.7 21.3 - - + -
131D ASP* 3.4 36.8 - - + +
134D GLY* 4.0 3.1 - - - +
136D SER* 1.3 71.9 - - - +
138D THR* 1.3 76.8 + - + +
139D LEU* 4.2 9.8 - - + +
183D THR* 3.3 2.6 + - - -
184D VAL 2.5 37.1 + - - +
185D THR 4.0 3.1 - - - +
186D SER* 3.5 31.2 - - - -
189D TRP* 4.4 14.8 - - + -
190D PRO* 5.1 5.4 - - + -
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Residues in contact with THR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR* 5.8 5.4 - - + -
116C SER* 3.8 25.0 + - - +
118C PHE* 3.0 31.6 - - + -
135C PHE* 5.2 4.0 - - - +
137C ASN* 6.0 0.7 + - - -
127D PRO* 4.1 5.9 - - - +
136D SER 4.4 5.4 - - - +
137D VAL* 1.3 85.5 - - - +
139D LEU* 1.3 63.8 + - - +
181D SER* 5.8 2.8 + - - -
182D VAL 3.6 4.0 - - - -
183D THR* 3.1 21.1 - - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C PHE* 4.5 3.6 - - - -
135C PHE* 5.4 0.7 - - - -
125D LEU 3.9 10.5 - - - +
127D PRO* 4.5 9.9 - - + -
137D VAL* 4.2 9.9 - - + +
138D THR* 1.3 87.4 + - - +
140D GLY* 1.3 57.8 + - - +
155D TRP* 4.5 9.0 - - + -
181D SER* 3.5 4.6 - - - -
182D VAL* 2.8 46.6 + - + +
184D VAL* 4.7 10.3 - - + -
189D TRP* 3.4 57.2 - - + +
194D ILE* 4.9 3.4 - - + -
211D ILE* 3.8 23.1 - - + -
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Residues in contact with GLY 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C PHE* 4.9 0.8 - - - -
135C PHE* 4.7 3.1 - - - -
123D TYR 3.8 0.5 - - - +
125D LEU* 3.0 49.1 + - - +
139D LEU* 1.3 76.7 - - - +
141D CYS* 1.3 58.4 + - - -
155D TRP* 3.6 9.4 - - - -
180D SER 3.5 10.5 - - - -
181D SER* 4.3 0.7 - - - -
211D ILE* 3.7 11.3 - - - +
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Residues in contact with CYS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D VAL* 4.2 21.3 - - - -
123D TYR 3.8 4.9 - - - -
125D LEU* 3.8 2.8 - - - +
140D GLY* 1.3 71.5 - - - -
142D LEU* 1.3 62.4 + - - +
143D VAL* 4.0 6.3 - - + +
153D LEU* 5.8 4.3 - - + -
155D TRP* 3.5 8.3 - - + -
179D SER* 3.8 3.1 - - - -
180D SER* 3.3 33.3 + - - +
196D CYS* 2.0 52.3 - - - -
198D VAL* 4.5 8.1 - - - -
209D LYS* 5.2 1.8 - - - -
211D ILE* 5.9 0.7 - - - -
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLN* 3.5 25.8 - - - +
131C SER* 3.7 18.6 - - - +
133C VAL* 5.0 15.0 - - + -
178C THR* 5.1 10.3 - - + +
121D PRO 4.3 1.6 - - - -
122D VAL* 3.3 21.3 - - - +
123D TYR* 3.5 29.2 + - + -
125D LEU* 3.8 22.8 - - + +
141D CYS* 1.3 71.1 - - - +
143D VAL* 1.3 78.3 + - - +
144D LYS* 5.3 2.9 - - + +
177D THR* 4.6 13.2 - - + -
178D LEU 3.9 10.3 - - - +
179D SER* 4.7 9.4 - - - +
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Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D PRO* 4.4 7.9 - - + -
121D PRO 3.5 6.7 - - - +
122D VAL* 4.7 13.5 - - + -
141D CYS* 4.0 8.1 - - + +
142D LEU* 1.3 85.3 - - - +
144D LYS* 1.3 60.9 + - - +
146D TYR* 3.5 28.9 - - + +
151D VAL* 5.0 8.1 - - + -
153D LEU* 5.7 2.5 - - + -
176D TYR 3.9 0.9 - - - +
177D THR* 3.0 4.3 - - - +
178D LEU* 2.7 66.9 + - + +
198D VAL* 5.0 14.4 - - + -
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Residues in contact with LYS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D PRO* 3.1 6.6 - - - +
121D PRO* 2.9 38.8 + - + +
123D TYR* 4.9 10.3 - - + +
142D LEU* 5.4 3.8 - - + -
143D VAL* 1.3 75.3 - - - +
145D GLY* 1.3 60.0 + - - +
172D GLN 5.3 2.6 + - - -
173D SER* 5.8 0.4 + - - -
175D LEU* 3.4 36.2 + - - +
177D THR* 3.5 30.2 + - + +
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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