Contacts of the strand formed by residues 73 - 79 (chain K) in PDB entry 5DSV
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 VAL 73 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68K ASN* 3.6 9.9 - - - +
69K VAL* 3.3 30.0 + - + -
70K ASP* 3.5 16.0 + - + +
71K ARG 3.4 0.2 - - - -
72K HIS* 1.3 112.2 - - + +
74K GLY* 1.3 70.0 - - - +
106K ILE* 4.9 1.3 - - + -
108K LEU* 3.7 32.3 - - + -
111K LEU* 4.1 20.2 - - + -
137K LEU* 4.3 6.7 - - + -
138K GLY 3.4 3.1 - - - +
139K SER* 4.2 0.2 - - - -
224K HIS* 4.0 4.0 - - - -
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Residues in contact with GLY 74 (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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47K PHE* 3.9 5.9 - - - -
67K PHE 3.4 7.2 - - - -
69K VAL 4.6 0.2 - - - -
73K VAL* 1.3 80.5 - - - +
75K MET* 1.3 60.1 + - - -
136K MET 3.5 0.7 - - - +
137K LEU* 3.2 5.9 - - - -
138K GLY 2.8 34.3 + - - -
224K HIS* 3.4 26.2 - - - -
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Residues in contact with MET 75 (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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47K PHE* 5.2 0.9 - - - -
65K ARG 3.8 0.3 - - - +
66K LEU* 3.3 7.3 - - - +
67K PHE* 2.9 41.6 + - + +
69K VAL* 3.7 29.8 - - + -
74K GLY* 1.3 75.0 - - - -
76K ALA* 1.3 63.8 + - - +
77K VAL* 3.6 26.2 - - + -
84K ALA* 3.9 21.8 - - - +
87K LEU* 4.4 4.9 - - + -
88K ALA* 3.8 22.9 - - + +
91K ALA* 4.9 3.4 - - - -
135K PHE* 3.7 27.4 - - + -
136K MET 3.2 4.5 - - - +
137K LEU* 3.8 16.2 - - + -
224K HIS* 4.6 0.7 + - - -
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Residues in contact with ALA 76 (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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36K ALA* 5.5 4.9 - - + -
37K ILE 5.5 1.3 - - - +
47K PHE* 3.6 28.3 - - + -
49K VAL* 5.2 2.5 - - + -
65K ARG 3.5 4.9 - - - +
66K LEU* 3.4 22.0 - - + -
75K MET* 1.3 75.9 - - - +
77K VAL* 1.3 61.4 + - - +
135K PHE* 3.1 2.3 - - - -
136K MET* 2.8 41.2 + - + +
165K ILE* 3.7 7.7 - - + +
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Residues in contact with VAL 77 (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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36K ALA* 4.2 5.2 - - - +
65K ARG* 3.1 47.1 + - + +
67K PHE* 3.8 26.5 - - + -
75K MET* 3.6 34.1 - - + -
76K ALA* 1.3 77.9 - - - +
78K ALA* 1.3 63.3 + - - +
81K LEU* 4.1 16.8 - - + -
84K ALA* 3.8 16.2 - - + -
134K SER 3.7 4.9 - - - +
135K PHE* 3.7 4.7 - - + -
165K ILE* 4.1 1.3 - - - -
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Residues in contact with ALA 78 (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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30K VAL* 3.8 13.8 - - + +
33K SER* 4.5 0.2 - - - +
34K SER 4.3 2.9 - - - +
36K ALA* 4.8 0.9 - - + -
65K ARG* 3.6 16.4 - - - +
77K VAL* 1.3 78.6 - - - +
79K GLY* 1.3 61.9 + - - +
133K CYS* 3.4 6.1 - - - +
134K SER 3.0 33.0 + - - +
165K ILE* 3.5 36.5 - - + +
166K GLY* 4.6 0.7 - - - -
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Residues in contact with GLY 79 (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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29K ALA 3.6 14.6 - - - -
30K VAL* 3.8 7.6 - - - +
33K SER* 3.1 34.6 + - - -
65K ARG* 5.8 0.9 - - - -
78K ALA* 1.3 72.7 - - - +
80K LEU* 1.3 64.9 + - - -
81K LEU* 3.2 9.4 + - - +
132K GLY 3.8 1.3 - - - -
133K CYS* 4.5 0.4 - - - -
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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