Contacts of the strand formed by residues 131 - 140 (chain K) in PDB entry 5LS6
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 GLU 131 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89J LEU* 4.1 6.8 - - + +
91J PHE* 3.1 50.6 - - + -
86K ASN* 4.6 0.7 - - - +
127K HIS* 2.9 29.6 + - + +
128K SER 5.0 3.9 - - - +
129K GLN 3.3 4.9 + - - +
130K GLY* 1.3 74.9 - - - +
132K ILE* 1.3 64.3 + - - +
133K ARG* 2.5 47.0 + - - +
436K ARG* 2.9 17.7 + - - -
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Residues in contact with ILE 132 (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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91J PHE* 5.7 0.2 - - - -
94J GLN* 2.7 29.3 + - - -
86K ASN* 4.1 10.6 + - + +
88K LEU* 3.6 37.1 - - + +
113K PHE* 4.3 7.6 - - + -
124K TYR* 3.6 34.5 - - + -
125K GLU 3.4 6.3 - - - +
126K CYS* 4.4 7.4 - - - -
130K GLY 3.4 5.2 + - - +
131K GLU* 1.3 83.4 - - - +
133K ARG* 1.3 54.4 + - - +
426K ILE* 4.3 12.1 - - + -
434K ILE* 5.2 2.2 - - + -
436K ARG* 3.9 35.9 - - + +
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Residues in contact with ARG 133 (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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70J ILE* 6.1 3.6 - - + -
94J GLN* 3.8 8.1 - - - +
124K TYR* 3.4 7.0 - - - +
125K GLU* 2.7 40.2 + - + +
127K HIS* 3.2 43.2 + - + +
131K GLU* 2.5 39.5 + - - +
132K ILE* 1.3 73.9 - - - +
134K LEU* 1.3 69.4 + - - +
135K LEU* 3.6 12.7 - - + +
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Residues in contact with LEU 134 (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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70J ILE* 4.6 4.2 - - - +
83J CYS* 3.8 17.9 - - + +
85J VAL* 3.3 28.5 - - + -
94J GLN* 2.6 39.5 + - + +
96J ILE* 3.8 30.6 - - + +
122K THR* 3.6 20.6 - - + -
123K LEU 3.7 7.0 - - - +
124K TYR* 3.4 32.1 - - + -
133K ARG* 1.3 76.9 - - - +
135K LEU* 1.3 63.3 + - - +
136K GLN 4.2 4.7 - - - +
137K SER* 5.3 1.1 - - - -
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Residues in contact with LEU 135 (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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68J VAL* 3.6 18.2 - - + -
69J HIS 3.6 17.3 - - - +
70J ILE* 3.4 30.6 - - + +
71J LEU 4.5 1.6 + - - +
96J ILE* 3.4 20.8 - - - +
112K VAL* 4.5 8.1 - - + -
123K LEU* 3.3 18.6 + - + +
124K TYR 4.3 1.6 - - - -
125K GLU* 3.4 51.1 - - + +
133K ARG* 3.6 14.6 - - + +
134K LEU* 1.3 80.8 - - - +
136K GLN* 1.3 75.6 + - + +
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Residues in contact with GLN 136 (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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69J HIS 4.4 12.6 + - - +
70J ILE* 4.8 2.4 - - - +
71J LEU 5.1 3.4 - - - +
96J ILE* 4.4 8.0 - - - +
122K THR* 3.4 6.4 - - - +
123K LEU* 2.9 40.6 + - + +
134K LEU* 3.9 2.2 - - - +
135K LEU* 1.3 89.1 - - + +
137K SER* 1.3 64.4 + - - +
138K TYR* 3.0 34.9 + - + -
177K PRO* 3.4 35.6 + - - +
180K MET* 3.5 29.7 - - - +
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Residues in contact with SER 137 (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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83J CYS* 3.4 21.5 - - - -
96J ILE* 4.1 11.2 - - - +
97J PRO 4.1 1.7 - - - +
98J LEU* 3.3 25.1 - - - +
99J LYS* 3.1 26.0 + - - +
120K ARG* 4.0 3.6 - - - -
121K VAL 3.3 6.8 + - - -
122K THR* 3.3 22.9 + - - -
134K LEU* 5.3 0.9 - - - -
136K GLN* 1.3 77.4 - - - +
138K TYR* 1.3 64.0 + - - +
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Residues in contact with TYR 138 (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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99J LYS* 3.1 37.5 - - + +
101J LEU* 3.8 25.2 - - + +
120K ARG* 2.9 22.7 - - - +
121K VAL* 2.8 45.3 + - + -
123K LEU* 4.7 12.3 - - + -
136K GLN* 3.0 47.3 + - + -
137K SER* 1.3 76.0 - - - +
139K VAL* 1.3 64.3 + - - +
175K ILE* 3.4 23.5 - - + +
177K PRO* 3.5 16.3 - - - +
180K MET* 3.6 16.5 - - + +
181K GLN* 5.5 0.7 - - - -
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Residues in contact with VAL 139 (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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81J ARG* 4.7 18.4 - - - +
98J LEU* 3.4 36.8 - - + -
99J LYS 2.8 11.3 + - - +
100J THR* 3.5 8.6 - - + +
101J LEU* 2.6 38.0 + - - +
119K ASN* 3.6 18.4 - - - +
120K ARG* 3.9 19.7 - - + +
138K TYR* 1.3 78.2 - - - +
140K ASP* 1.3 75.1 + - - +
141K ALA* 3.5 1.7 + - - +
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Residues in contact with ASP 140 (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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101J LEU* 3.6 7.3 - - - +
103J ALA* 5.1 0.9 + - - -
104J VAL 5.4 0.2 + - - -
119K ASN* 3.0 18.0 + - - +
139K VAL* 1.3 81.8 - - - +
141K ALA* 1.3 65.6 + - - +
142K ASP* 3.0 32.6 + - - +
143K ALA 4.2 0.2 + - - -
145K GLU* 3.4 30.3 - - + +
147K PHE* 3.5 15.7 - - + -
169K ARG* 4.2 4.7 + - - -
173K ARG* 2.6 46.3 + - - -
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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