Contacts of the strand formed by residues 149 - 154 (chain h) in PDB entry 5GJQ
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 PRO 149 (chain h).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43h ARG* 3.5 19.2 + - + -
44h GLY 3.3 25.8 - - - +
45h LYS 4.3 11.2 - - - +
47h CYS 3.3 33.7 - - - +
48h ALA* 4.5 0.9 - - + -
142h GLY 3.8 4.9 - - - +
143h ILE* 3.8 14.3 - - + -
147h GLN 4.1 4.8 - - - +
148h GLY* 1.3 86.7 - - - +
150h GLN* 1.3 70.8 + - - +
222h VAL* 5.2 5.2 - - + -
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Residues in contact with GLN 150 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43h ARG* 4.5 13.4 - - - +
48h ALA* 4.2 2.6 - - - +
111h VAL* 4.4 13.2 - - + -
112h ASP* 4.6 8.5 + - - +
140h LEU 4.3 0.4 - - - -
141h ILE* 3.2 7.8 - - - +
142h GLY 2.8 38.4 + - - +
144h ASP* 4.1 14.4 - - + +
147h GLN* 3.9 33.3 + - - +
148h GLY 3.9 9.6 - - - +
149h PRO* 1.3 90.2 + - - +
151h VAL* 1.3 66.7 + - - +
152h TYR* 3.3 37.6 + - + -
72p ARG* 5.2 1.9 + - - -
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Residues in contact with VAL 151 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41h ALA* 4.0 9.6 - - + +
42h VAL 4.4 10.5 - - - +
43h ARG* 4.0 27.4 + - + +
48h ALA* 4.3 6.3 - - + -
139h ILE* 4.0 21.5 - - + -
140h LEU 3.3 3.8 - - - +
141h ILE* 3.8 13.5 - - + -
150h GLN* 1.3 79.5 + - - +
152h TYR* 1.3 69.2 + - - +
162h GLY* 3.3 4.5 - - - -
163h PHE* 2.9 38.2 + - + +
164h LYS 5.3 0.4 - - - +
165h ALA* 5.7 0.2 - - - -
166h THR* 4.0 20.9 - - - +
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Residues in contact with TYR 152 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111h VAL* 3.8 26.0 - - + -
112h ASP* 3.9 37.3 + - + +
115h CYS* 3.9 14.4 - - + -
139h ILE* 3.2 8.0 - - - +
140h LEU* 2.8 31.8 + - + +
147h GLN* 4.8 4.3 + - - -
150h GLN* 3.3 38.8 + - + -
151h VAL* 1.3 80.0 - - - +
153h LYS* 1.3 61.9 + - - +
160h TYR* 4.1 19.1 - + - -
161h CYS 3.3 17.9 - - - -
162h GLY* 3.6 17.9 - - - -
163h PHE* 5.0 0.2 - - - -
60i SER* 3.7 23.2 + - - -
61i VAL* 5.3 0.7 - - + -
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Residues in contact with LYS 153 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115h CYS* 3.7 2.9 - - - -
137h CYS* 3.6 22.4 - - - -
138h MET 3.2 7.2 - - - +
139h ILE* 3.6 32.1 - - + -
152h TYR* 1.3 78.3 - - - +
154h CYS* 1.3 64.6 + - - +
155h ASP* 4.1 13.6 - - - +
159h TYR 3.9 0.2 - - - +
160h TYR* 3.0 4.3 - - - +
161h CYS* 2.9 29.8 + - - +
163h PHE* 3.8 23.2 - - + -
166h THR* 4.1 19.6 - - + +
167h ALA 3.4 19.9 + - - -
168h ALA* 4.7 1.5 - - - +
172h GLN* 3.5 19.4 - - - +
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Residues in contact with CYS 154 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90h GLN* 4.5 4.3 - - - -
115h CYS* 3.6 19.5 - - - +
118h ILE* 3.9 25.1 - - - -
119h ALA* 4.3 12.3 - - + -
137h CYS* 3.7 11.4 - - - -
138h MET* 2.9 51.4 + - - -
153h LYS* 1.3 74.1 - - - +
155h ASP* 1.3 69.5 + - - +
159h TYR 3.2 7.6 - - - +
160h TYR* 4.0 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