Contacts of the strand formed by residues 88 - 92 (chain K) in PDB entry 6CNC
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 PHE 88 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577A THR* 3.0 37.7 - - + -
580A LEU* 3.6 29.4 - - + -
581A SER* 3.3 34.8 - - - -
590A PHE* 3.7 16.2 - + - -
592A ILE* 4.2 11.0 - - + -
86K VAL* 4.7 0.7 - - - -
87K GLU* 1.3 75.1 - - - +
89K CYS* 1.3 59.5 + - - +
90K GLY 5.0 0.2 - - - -
104K ARG* 3.1 36.6 - - + +
105K ILE* 3.1 1.9 - - - +
106K GLN* 2.9 64.7 + - + +
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Residues in contact with CYS 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A THR* 3.2 14.3 - - - +
578A GLN 4.9 0.5 + - - -
77K ARG* 4.1 17.0 + - - +
80K ILE* 3.5 33.0 - - + -
81K MET* 3.4 52.8 - - - +
86K VAL* 3.6 9.4 - - + -
87K GLU 3.8 0.2 + - - -
88K PHE* 1.3 74.6 - - - +
90K GLY* 1.3 57.8 + - - +
103K ILE* 5.5 0.7 - - + -
104K ARG 2.9 8.1 - - - +
105K ILE* 4.1 5.8 - - + -
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Residues in contact with GLY 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578A GLN* 4.5 11.4 - - - -
581A SER* 2.9 28.5 + - - -
77K ARG* 4.9 3.1 - - - -
88K PHE* 4.2 0.8 - - - -
89K CYS* 1.3 74.6 - - - +
91K TYR* 1.3 64.7 + - - -
102K ASN 3.9 0.3 - - - +
103K ILE* 3.6 4.2 - - - +
104K ARG* 2.9 31.0 + - - +
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Residues in contact with TYR 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578A GLN* 4.0 19.3 + - - +
581A SER* 3.4 5.1 + - - -
582A MET* 3.9 16.5 - - - +
1008B ILE 4.2 3.6 + - - -
70K HIS* 3.1 37.6 + + - -
73K GLY* 3.2 31.0 - - - -
74K ASN* 3.0 34.2 + - - +
77K ARG* 3.5 26.5 - - + -
90K GLY* 1.3 76.0 - - - +
92K SER* 1.3 66.1 + - - +
101K LEU* 3.5 26.5 - - + -
102K ASN 3.0 12.1 - - - +
103K ILE* 3.9 14.8 - - + -
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Residues in contact with SER 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A SER 4.5 0.2 - - - -
582A MET* 4.1 15.0 - - - -
585A ASP* 3.5 28.0 + - - +
703A ARG* 3.1 34.0 + - - +
70K HIS* 5.6 1.3 - - - -
91K TYR* 1.3 79.8 - - - +
93K ILE* 1.3 63.8 + - - +
94K PRO* 3.5 4.2 - - - +
101K LEU* 3.7 2.4 - - - +
102K ASN* 2.9 33.2 + - - +
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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