Contacts of the strand formed by residues 85 - 90 (chain A) in PDB entry 6YBO
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 LYS 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A HIS* 3.1 42.6 + - + +
50A GLY* 3.1 1.0 - - - -
51A VAL* 2.9 26.7 + - - +
79A LEU* 5.8 0.4 - - - -
83A GLY* 3.6 23.3 + - - +
84A MET* 1.3 77.4 + - - +
86A VAL* 1.3 68.1 + - - +
87A PRO* 3.6 9.0 - - + -
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Residues in contact with VAL 86 (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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51A VAL* 3.3 13.9 - - + +
53A PHE* 3.7 31.4 - - + -
75A PHE* 4.1 13.0 - - + -
79A LEU* 3.7 33.2 - - + -
85A LYS* 1.3 80.6 - - - +
87A PRO* 1.3 59.0 - - - +
88A MET 3.8 11.7 - - - +
129A LEU* 4.0 22.2 + - + +
130A GLY 3.6 4.4 - - - +
131A ALA* 3.1 27.1 + - + -
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Residues in contact with PRO 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 4.2 11.2 - - - +
12A THR* 4.0 23.6 - - + -
49A HIS* 4.3 15.5 - - + +
51A VAL 3.5 16.8 - - - +
52A THR* 4.6 2.7 - - + -
85A LYS* 3.6 7.9 - - + +
86A VAL* 1.3 88.5 - - - +
88A MET* 1.3 59.7 + - + +
130A GLY 4.8 1.6 - - - +
131A ALA* 3.8 2.5 - - - -
132A GLU* 3.0 32.8 + - + +
133A THR* 3.3 9.7 + - - -
283A PRO* 3.9 22.3 - - + +
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Residues in contact with MET 88 (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 TRP* 4.4 7.2 - - + -
52A THR* 3.3 39.5 - - + +
86A VAL* 3.3 8.7 + - - +
87A PRO* 1.3 81.7 - - + +
89A ALA* 1.3 91.2 + - - +
90A THR* 4.3 5.4 - - + -
131A ALA* 4.0 4.7 - - - -
133A THR* 3.2 16.4 - - - +
135A VAL* 3.6 33.4 - - + -
215A ASN* 5.2 0.4 - - - +
243A HIS* 3.7 42.0 - - + +
245A ASP* 4.9 2.2 - - - +
285A HIS* 3.7 21.3 - - + -
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Residues in contact with ALA 89 (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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53A PHE* 3.4 37.9 - - + +
88A MET* 1.3 79.7 - - - +
90A THR* 1.3 64.2 + - - +
122A ASN* 4.2 1.1 - - - +
126A ALA* 3.7 26.0 - - + -
131A ALA* 4.2 2.1 - - + +
133A THR 3.3 5.5 + - - -
134A TYR* 3.3 13.6 - - + -
135A VAL 3.0 23.7 + - - -
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Residues in contact with THR 90 (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 TRP* 4.6 6.1 - - + -
53A PHE 2.9 15.9 + - - +
54A HIS* 3.2 35.2 + - + +
55A ASP 3.1 12.6 + - - -
88A MET* 4.3 7.0 - - + -
89A ALA* 1.3 76.8 - - - +
91A THR* 1.3 68.4 + - - +
122A ASN* 2.9 17.2 + - - -
134A TYR* 3.4 10.5 - - - -
135A VAL* 2.7 38.7 + - + +
136A ALA* 4.4 2.8 - - - -
137A TRP* 4.6 3.8 + - - +
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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