Contacts of the strand formed by residues 135 - 140 (chain P) 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 THR 135 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P GLY 3.5 6.5 + - - +
134P THR* 1.3 77.7 - - - +
136P CYS* 1.3 63.7 + - - +
160P LEU 3.8 4.3 - - - +
161P HIS* 3.8 20.0 - - + +
185P ARG* 4.8 4.5 - - - +
202P ASN* 3.5 32.4 + - - +
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Residues in contact with CYS 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H TYR* 4.8 1.4 + - - -
134P THR 3.7 10.8 - - - -
135P THR* 1.3 75.6 - - - +
137P TYR* 1.3 69.4 + - - +
159P ASP* 3.7 7.3 - - - +
160P LEU* 2.8 32.6 + - + +
161P HIS* 4.6 0.4 - - - -
162P VAL* 3.9 11.9 - - - -
183P ALA* 5.4 0.2 - - - -
199P LEU* 3.8 19.3 - - + -
200P VAL 3.6 8.3 - - - +
201P CYS* 2.1 47.8 - - - -
202P ASN 5.2 0.2 - - - +
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Residues in contact with TYR 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H TYR* 4.0 47.0 - + + +
27P GLN* 3.3 25.5 + - - -
29P TRP* 4.5 6.8 - - - -
136P CYS* 1.3 81.0 - - - +
138P ALA* 1.3 69.3 + - - +
139P SER* 5.1 2.9 - - - -
157P CYS* 3.8 32.5 - - + -
158P VAL 3.3 18.6 - - - +
159P ASP* 4.2 2.9 - - - +
160P LEU* 4.4 4.0 - - - +
199P LEU* 3.7 1.3 - - - +
200P VAL* 3.0 61.6 + - + +
202P ASN 6.1 0.9 - - - -
203P GLY* 5.9 4.3 - - - -
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Residues in contact with ALA 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P TYR* 1.3 84.4 - - - +
139P SER* 1.3 61.0 + - - +
156P GLN 3.4 9.6 - - - +
158P VAL* 3.4 23.2 + - + +
160P LEU* 4.3 7.9 - - + -
192P SER* 4.3 7.2 + - - +
197P GLY 5.7 0.7 - - - +
198P PRO 3.2 18.6 - - - +
199P LEU* 3.9 9.4 - - + -
200P VAL* 5.0 0.2 - - - -
228P TYR* 4.1 21.5 - - + +
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Residues in contact with SER 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P GLN* 4.6 9.8 + - - -
29P TRP* 5.5 0.5 + - - -
30P GLN* 2.6 35.1 + - - +
137P TYR* 4.8 2.9 - - - -
138P ALA* 1.3 74.5 - - - +
140P GLY* 1.3 59.1 + - - +
155P LEU* 4.2 13.2 - - - -
156P GLN 3.1 11.4 - - - -
157P CYS* 4.2 14.1 - - - -
192P SER* 4.9 4.8 - - - -
193P GLY 5.3 0.5 - - - -
194P ASP 5.1 1.9 - - - +
197P GLY* 3.9 10.7 - - - -
198P PRO* 3.5 20.6 + - - +
200P VAL* 5.8 1.7 - - - +
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Residues in contact with GLY 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P GLN* 4.6 4.5 - - - -
139P SER* 1.3 78.5 - - - +
141P TRP* 1.3 62.1 + - - -
155P LEU* 3.5 13.0 - - - +
156P GLN* 3.0 23.3 + - - +
192P SER 3.0 20.8 + - - +
193P GLY* 3.8 10.1 - - - -
194P ASP* 4.1 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