Contacts of the strand formed by residues 135 - 140 (chain A) in PDB entry 5A8Z
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 GLN 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLY 3.3 17.0 - - - +
134A VAL* 1.3 77.4 - - - +
136A CYS* 1.3 58.1 + - - +
159A ASN* 4.9 3.0 - - - +
160A VAL 3.7 5.8 + - - -
161A THR* 3.0 28.3 + - - +
201A CYS* 4.3 0.7 - - - -
202A ASN* 4.3 4.1 + - - +
1B NAG 2.8 36.7 + - - +
2B FUC 2.5 39.4 + - - +
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Residues in contact with CYS 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 VAL* 4.1 3.1 - - - -
135A GLN* 1.3 77.4 + - - +
137A LEU* 1.3 62.0 + - - +
159A ASN* 3.6 9.5 + - - +
160A VAL* 2.8 37.6 + - + +
162A VAL* 3.7 26.7 - - - -
183A THR* 5.0 0.4 - - - -
199A LEU* 3.7 16.2 - - + -
200A VAL 3.2 5.6 - - - +
201A CYS* 2.0 48.0 - - - -
1B NAG 5.3 0.2 - - - -
2B FUC 3.8 4.3 - - - -
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Residues in contact with LEU 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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20A ARG* 3.6 25.4 - - - +
27A TRP* 3.2 46.0 - - + -
136A CYS* 1.3 72.7 - - - +
138A ALA* 1.3 68.6 + - - +
139A MET* 4.4 5.2 - - + +
157A GLU* 4.0 10.8 - - + +
158A LEU 3.5 20.9 - - - +
159A ASN* 3.7 7.0 - - - +
198A PRO 4.1 1.4 - - - +
199A LEU* 3.6 5.4 - - - -
200A VAL* 2.8 43.1 + - + +
1B NAG 4.1 14.4 - - - +
2B FUC 4.3 15.5 - - - -
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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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16A ILE* 4.3 4.5 - - + -
136A CYS 4.0 0.6 - - - -
137A LEU* 1.3 75.2 - - - +
139A MET* 1.3 64.5 + - - +
157A GLU* 3.3 3.5 - - - +
158A LEU* 2.8 33.0 + - + +
160A VAL* 4.0 22.8 - - + +
190A VAL* 4.0 24.9 - - + -
198A PRO 4.2 3.8 - - - -
199A LEU* 3.9 15.3 - - + +
228A PHE* 4.4 4.7 - - + -
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Residues in contact with MET 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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16A ILE* 3.7 15.1 - - - +
27A TRP* 3.6 53.4 - - + +
29A PHE* 4.1 1.3 - - - -
30A MET* 4.0 19.7 - - - +
137A LEU* 4.4 15.9 - - + +
138A ALA* 1.3 77.1 - - - +
140A GLY* 1.3 58.8 + - - +
155A LEU* 4.6 4.5 - - + -
156A GLN 3.1 17.0 - - - +
157A GLU* 4.1 3.4 - - + -
190A VAL* 5.4 1.4 - - - +
194A ASP* 4.3 1.6 - - - +
197A SER* 3.1 24.8 - - - -
198A PRO* 3.7 29.1 + - - +
200A VAL* 3.8 23.6 - - + -
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Residues in contact with GLY 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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16A ILE* 3.6 4.5 + - - +
30A MET* 4.0 3.8 - - - -
139A MET* 1.3 76.3 - - - +
141A TRP* 1.3 58.0 - - - -
142A GLY 3.8 1.2 + - - -
155A LEU* 3.7 15.8 - - - +
156A GLN* 3.0 36.3 + - - +
194A ASP* 3.3 15.0 - - - -
197A SER* 3.9 9.0 - - - -
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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