Contacts of the strand formed by residues 50 - 58 (chain K) in PDB entry 5D4D
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 GLY 50 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49K PRO* 1.3 75.9 - - - +
51K THR* 1.3 69.9 + - - +
146K ARG* 3.4 8.1 + - - +
147K GLY 3.0 30.0 + - - -
171K PHE* 3.4 15.0 + - - -
173K PRO* 3.9 9.6 - - - -
204K SER* 4.9 3.8 - - - -
205K VAL* 5.3 4.3 - - - -
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Residues in contact with THR 51 (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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50K GLY* 1.3 80.2 - - - +
52K ALA* 1.3 64.3 + - - +
85K LEU 4.8 6.6 - - - +
86K VAL* 5.7 0.7 - - - -
87K VAL* 2.4 38.0 + - - +
89K PHE* 4.0 30.7 - - + +
144K VAL* 4.2 8.5 - - - -
145K ASP 3.2 13.2 - - - +
146K ARG* 4.0 12.8 - - + +
170K VAL 4.3 1.4 - - - +
171K PHE* 3.4 11.9 + - - +
173K PRO* 5.9 0.2 - - - +
202K ASP* 5.4 3.5 - - - +
204K SER* 3.5 13.5 + - - +
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Residues in contact with ALA 52 (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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51K THR* 1.3 77.3 - - - +
53K VAL* 1.3 63.8 + - - +
54K THR* 3.3 4.6 + - - +
83K LYS 6.0 2.2 - - - +
85K LEU 5.0 7.2 - - - +
144K VAL* 3.9 7.2 - - - +
145K ASP 3.0 29.3 + - - +
168K ASP 5.6 0.2 - - - +
169K ALA* 4.1 4.3 - - + -
170K VAL 3.3 33.0 - - - +
171K PHE* 3.8 15.7 - - + -
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Residues in contact with VAL 53 (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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52K ALA* 1.3 72.6 - - - +
54K THR* 1.3 58.8 - - - +
55K SER 3.6 22.7 - - - +
56K VAL* 3.8 17.0 - - + -
82K LEU* 3.2 31.4 - - + +
83K LYS* 5.2 4.1 - - - +
85K LEU* 3.8 20.8 + - + +
142K VAL* 4.0 8.5 - - + -
143K ARG 3.6 6.3 - - - +
144K VAL* 3.7 19.1 - - + -
167K VAL* 3.5 22.8 - - + +
168K ASP 3.9 8.5 - - - +
169K ALA* 4.4 1.9 - - - +
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Residues in contact with THR 54 (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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52K ALA 3.3 8.0 + - - +
53K VAL* 1.3 73.3 - - - +
55K SER* 1.3 58.8 + - - -
143K ARG* 2.6 18.7 + - - +
145K ASP* 2.8 43.7 + - + -
156K HIS* 3.3 18.0 - - + +
158K ILE* 3.9 21.4 - - + +
166K PRO* 3.8 0.3 - - - +
167K VAL* 2.9 24.9 + - - -
169K ALA* 3.8 21.1 - - + -
171K PHE* 4.0 8.7 - - + -
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Residues in contact with SER 55 (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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53K VAL* 3.6 3.3 - - - +
54K THR* 1.3 82.0 - - - +
56K VAL* 1.3 74.0 + - - +
141K GLU 4.8 0.4 - - - -
142K VAL* 3.5 0.3 - - - -
143K ARG* 2.8 38.5 + - - +
158K ILE* 3.2 32.4 + - - -
159K LYS* 4.2 1.3 - - - -
160K ASP* 4.5 3.0 + - - -
164K ALA* 3.6 20.3 - - - +
165K ILE 3.6 8.4 + - - -
167K VAL* 3.8 2.2 - - - -
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Residues in contact with VAL 56 (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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53K VAL* 3.8 16.6 - - + -
55K SER* 1.3 85.2 + - - +
57K TYR* 1.3 62.9 + - - +
58K ILE* 3.9 24.9 - - + -
79K ILE* 4.7 13.9 - - + -
82K LEU* 3.5 35.2 - - + -
140K MET* 4.6 3.6 - - - -
141K GLU 3.8 3.8 - - - +
142K VAL* 4.0 7.2 - - + -
164K ALA* 4.4 0.2 - - - -
165K ILE* 2.8 44.9 + - + +
167K VAL* 3.8 12.3 - - + -
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Residues in contact with TYR 57 (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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56K VAL* 1.3 73.4 - - - +
58K ILE* 1.3 77.9 + - - +
59K GLU* 3.7 30.2 - - + +
60K ASP 4.6 2.4 + - - -
139K ASN* 4.9 3.6 - - - -
140K MET* 3.2 6.2 - - - +
141K GLU* 2.9 61.2 + - + +
161K ARG* 3.4 51.0 + - + -
163K ASN* 3.5 40.3 + - + -
164K ALA* 4.5 8.3 - - + +
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Residues in contact with ILE 58 (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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56K VAL* 3.9 12.1 + - + -
57K TYR* 1.3 89.3 - - - +
59K GLU* 1.3 76.5 + - - +
61K VAL* 3.2 34.0 + - + +
68K ILE* 3.6 34.8 - - + -
75K VAL* 4.2 22.2 - - + -
78K ILE* 4.3 14.6 - - + -
138K LEU* 3.8 13.2 - - + -
139K ASN 3.4 7.6 - - - +
140K MET* 3.6 22.0 - - + -
163K ASN 5.3 0.8 + - - -
165K ILE* 5.4 1.7 - - + +
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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