Contacts of the strand formed by residues 138 - 145 (chain A) in PDB entry 1QXP
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 ILE 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 2.7 37.3 + - + +
35A LEU* 3.5 32.8 - - + +
36A ARG* 3.7 36.3 - - + -
39A CYS* 5.6 0.2 - - - -
46A PHE* 3.5 30.5 - - + -
135A TYR 4.5 3.3 + - - +
136A ALA* 4.2 5.4 - - + +
137A GLY* 1.4 86.6 - - - +
139A PHE* 1.3 79.3 + - - +
153A VAL* 3.9 15.5 - - + -
154A VAL 3.3 10.3 - - - +
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Residues in contact with PHE 139 (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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32A TYR* 4.1 2.9 - - - -
87A PHE* 3.6 31.6 - + + -
129A GLN* 2.9 24.2 - - + +
130A SER 3.4 30.5 - - - -
131A PHE* 3.3 33.0 - + - -
135A TYR* 4.0 6.5 - + - -
138A ILE* 1.3 86.3 - - - +
140A HIS* 1.3 61.2 + - - +
141A PHE* 4.4 6.7 - - + -
153A VAL* 3.4 2.8 - - - +
154A VAL* 2.8 37.3 + - + +
156A ASP* 3.4 37.0 - - + -
180A LEU* 3.4 19.1 - - + -
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Residues in contact with HIS 140 (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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32A TYR* 3.6 36.9 - + + -
33A GLU* 5.2 3.2 + - - -
126A PRO* 3.2 34.0 - - + +
127A TYR 5.4 2.0 - - - -
129A GLN* 2.7 41.5 + - + +
139A PHE* 1.3 74.2 - - - +
141A PHE* 1.3 73.0 + - - +
142A GLN* 4.9 1.6 + - - -
151A ASP* 2.9 29.9 + - - +
152A VAL 3.4 9.0 - - - +
153A VAL* 3.4 24.5 - - + -
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Residues in contact with PHE 141 (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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87A PHE* 4.2 14.4 - + - -
124A VAL 3.7 4.5 - - - +
125A VAL* 3.6 39.9 - - + -
126A PRO* 4.4 2.2 - - - -
139A PHE* 4.4 4.3 - - + -
140A HIS* 1.3 80.4 - - - +
142A GLN* 1.3 74.5 + - - +
143A LEU* 4.8 3.8 - - + -
151A ASP* 3.2 2.5 - - - +
152A VAL* 2.7 35.5 + - + +
154A VAL* 4.2 10.8 - - + -
177A TRP 3.7 7.4 - - - -
180A LEU* 3.4 31.4 - - + -
181A LEU* 3.1 41.7 - - + -
184A ALA* 3.8 20.2 - - + -
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Residues in contact with GLN 142 (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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21A HIS* 2.9 43.9 + - - +
24A ALA* 4.6 6.8 - - - +
123A ARG 3.4 10.3 + - - +
124A VAL* 3.0 36.9 + - - +
126A PRO* 5.0 15.3 - - + +
140A HIS* 4.9 3.5 + - - -
141A PHE* 1.3 83.4 - - - +
143A LEU* 1.4 61.0 + - - +
149A TRP* 3.4 14.5 - - + -
150A VAL 3.4 6.1 - - - +
151A ASP* 2.4 39.8 - - - +
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Residues in contact with LEU 143 (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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124A VAL* 4.0 1.3 - - + -
141A PHE* 4.8 2.5 - - + -
142A GLN* 1.4 80.8 - - - +
144A TRP* 1.3 67.1 + - - +
145A GLN* 3.5 11.7 + - + +
149A TRP* 3.4 7.2 - - - -
150A VAL* 3.2 32.3 + - + +
152A VAL* 4.2 12.1 - - + -
181A LEU* 4.0 16.6 - - + -
184A ALA* 4.1 14.6 - - + +
185A TYR* 4.2 18.8 - - + -
188A VAL* 3.8 28.3 - - + -
206A ASP 3.6 5.6 - - - +
207A PHE* 3.9 28.3 - - + -
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Residues in contact with TRP 144 (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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143A LEU* 1.3 68.9 - - - +
145A GLN* 1.3 82.4 + - - +
146A PHE 4.0 7.2 - - - -
147A GLY* 3.3 38.4 + - - -
148A GLU 4.0 2.2 - - - -
149A TRP* 3.5 30.1 - + + +
205A GLU* 3.5 23.8 - - + +
206A ASP* 2.8 36.4 + - - +
209A GLY* 3.2 29.7 + - - +
210A GLY 4.9 0.2 - - - -
343A LEU* 5.0 3.4 - - - +
414A MET* 3.6 30.3 - - + -
470A ARG* 5.1 0.4 - - - -
499A LEU* 4.1 9.9 - - + -
501A ARG* 3.6 35.9 - - - -
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Residues in contact with GLN 145 (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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27A TYR* 5.8 3.0 - - + -
143A LEU* 4.0 17.5 - - + +
144A TRP* 1.3 97.4 + - - +
146A PHE* 1.4 92.4 + - + +
147A GLY 3.2 0.4 - - - -
148A GLU* 2.9 41.9 + - + +
150A VAL* 4.5 14.8 - - + -
185A TYR* 4.5 4.9 - - - -
188A VAL* 3.6 30.9 - - + +
189A ASN* 4.6 8.0 + - - +
206A ASP* 3.3 25.0 + - - +
470A ARG* 5.5 0.8 - - - +
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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