Contacts of the strand formed by residues 81 - 89 (chain K) in PDB entry 5HJD
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 81 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32K TRP* 4.0 15.9 - + - -
55K LEU* 4.0 2.9 - - + -
56K HIS* 3.6 32.8 - - + -
59K PHE* 3.8 24.5 - + - -
79K ALA 3.8 7.6 - - - -
80K GLY* 1.3 79.7 - - - +
82K ILE* 1.3 73.7 + - - +
83K LEU* 3.6 27.6 - - + -
104K LEU* 2.9 57.9 + - + +
17M ARG* 3.8 14.1 - - - +
18M KCR 3.8 32.1 - - + +
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Residues in contact with ILE 82 (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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54K HIS 5.0 1.2 - - - +
55K LEU 5.7 0.3 - - - -
56K HIS* 5.6 0.7 + - - -
81K PHE* 1.3 82.8 - - - +
83K LEU* 1.3 60.5 + - - +
84K PRO* 3.1 22.4 - - + +
101K ASP* 4.1 25.1 - - + +
102K TYR 3.6 2.0 - - - +
103K ASP* 3.6 35.7 - - + +
17M ARG* 4.2 10.1 - - - +
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Residues in contact with LEU 83 (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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32K TRP* 4.7 0.4 - - + -
34K VAL* 4.1 16.2 - - + -
53K PHE* 3.8 24.0 - - + -
54K HIS 3.6 15.7 - - - +
55K LEU* 3.6 19.5 - - + -
81K PHE* 3.6 23.3 + - + -
82K ILE* 1.3 73.4 - - - +
84K PRO* 1.3 77.0 - - - +
85K ILE* 3.2 13.5 - - + +
102K TYR* 2.6 34.7 + - + +
104K LEU* 4.0 28.5 - - + -
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Residues in contact with PRO 84 (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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54K HIS* 3.4 44.0 + - + +
82K ILE* 3.1 22.0 - - + +
83K LEU* 1.3 86.2 - - - +
85K ILE* 1.3 58.9 + - - +
99K ARG* 3.5 21.1 - - - +
100K PHE 3.2 9.4 - - - +
101K ASP* 3.3 22.7 - - - +
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Residues in contact with ILE 85 (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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13K LEU* 3.8 26.7 - - + -
34K VAL* 4.4 9.6 - - + -
35K PHE 5.2 0.2 - - - +
36K VAL* 3.9 10.3 - - + -
51K VAL* 3.8 27.1 - - + -
52K VAL 3.5 6.1 - - - +
53K PHE* 3.9 21.3 - - + -
83K LEU* 3.2 21.8 - - + +
84K PRO* 1.3 74.6 - - - +
86K GLU* 1.3 67.6 + - - +
87K VAL* 4.2 4.3 - - + -
98K VAL 3.7 0.9 - - - +
99K ARG* 3.5 5.0 - - - -
100K PHE* 2.6 39.0 + - + +
102K TYR* 3.8 22.2 - - + -
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Residues in contact with GLU 86 (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 LYS 3.9 0.7 - - - +
51K VAL* 3.4 3.5 - - - +
52K VAL* 2.7 46.1 + - + +
54K HIS* 3.2 28.5 + - - +
63K LYS* 4.9 1.7 + - - -
85K ILE* 1.3 77.6 - - - +
87K VAL* 1.3 62.6 + - - +
88K TYR* 2.9 36.8 + - + -
97K LYS* 3.2 28.2 + - + -
98K VAL 3.5 6.5 - - - +
99K ARG* 4.1 26.5 + - + +
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Residues in contact with VAL 87 (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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11K LEU* 4.3 15.7 - - + -
36K VAL* 4.3 22.7 - - + -
48K VAL* 3.9 27.4 - - + -
50K LYS 3.8 2.2 - - - -
51K VAL* 4.3 17.0 - - + +
85K ILE* 4.5 7.0 - - + -
86K GLU* 1.3 74.5 - - - +
88K TYR* 1.3 66.9 + - - +
89K PHE* 3.9 15.2 - - + -
97K LYS* 3.2 3.0 - - - -
98K VAL* 3.1 42.3 + - + -
100K PHE* 4.4 9.6 - - + -
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Residues in contact with TYR 88 (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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48K VAL* 3.5 6.8 - - - +
49K GLU* 2.7 37.8 + - - +
50K LYS* 2.9 52.2 + - + +
52K VAL* 3.8 16.8 - - + +
63K LYS* 5.4 3.6 + - - -
86K GLU* 2.9 38.5 + - + -
87K VAL* 1.3 77.7 - - - +
89K PHE* 1.3 56.6 + - - +
96K ARG* 3.4 29.8 - - + +
97K LYS* 3.4 39.7 + - + +
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Residues in contact with PHE 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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47K PHE* 3.1 29.2 - + - +
49K GLU* 3.6 7.9 - - - +
87K VAL* 3.9 20.2 - - + -
88K TYR* 1.3 76.2 - - - +
90K LYS* 1.3 53.1 + - - +
91K ASN* 2.7 29.6 + - + -
95K PRO* 3.4 27.4 - - + -
96K ARG* 3.0 33.7 + - - +
97K LYS* 3.7 19.7 - - - -
98K VAL* 3.7 24.5 - - + -
122K LEU* 4.2 12.1 - - + -
124K PHE* 3.8 31.2 - + - -
131K PHE* 3.9 8.5 - + + -
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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