Contacts of the strand formed by residues 113 - 124 (chain B) in PDB entry 6A5T
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 SER 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B MET* 5.6 1.8 - - - -
84B LEU* 5.2 6.5 - - - -
85B SER 3.8 14.7 + - - -
86B ARG* 4.8 0.2 - - - -
87B PRO* 3.6 15.2 - - - +
112B SER* 1.3 78.8 + - - +
114B PRO* 1.3 71.6 - - - +
115B VAL* 3.6 1.9 + - - +
160B LYS* 3.2 5.8 - - - -
161B VAL* 2.8 38.8 + - - +
163B ILE* 3.3 28.0 - - - +
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Residues in contact with PRO 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.3 13.7 - - - +
85B SER* 4.2 12.2 + - - +
86B ARG 4.3 12.6 - - - +
88B THR* 4.5 18.6 - - - +
112B SER 4.1 5.2 - - - +
113B SER* 1.3 86.7 - - - +
115B VAL* 1.3 60.3 + - - +
116B TYR* 3.9 21.8 + - + +
157B HIS* 3.8 25.6 - - + -
159B GLY 3.5 7.0 - - - +
160B LYS* 4.3 16.2 - - + -
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 5.3 7.6 - - + -
82B ILE* 3.8 23.6 - - + -
84B LEU* 3.5 21.3 - - + -
113B SER 3.6 8.5 - - - +
114B PRO* 1.3 77.1 - - - +
116B TYR* 1.3 64.0 + - - +
117B LEU* 5.7 0.2 - - + -
156B VAL 3.4 9.4 - - - +
158B ILE* 3.5 32.7 + - + +
159B GLY 2.9 21.7 + - - +
161B VAL* 3.7 28.3 - - + +
410B PHE* 5.5 5.8 - - + -
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Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS 4.1 0.3 - - - +
82B ILE* 3.6 6.2 - - - +
83B TYR* 2.9 50.5 + - + +
85B SER* 5.3 14.4 - - - -
114B PRO* 3.9 19.8 - - + +
115B VAL* 1.3 73.8 - - - +
117B LEU* 1.3 59.0 + - - +
155B LYS* 4.2 33.2 - - + -
156B VAL 3.4 1.6 - - - -
157B HIS* 3.3 51.6 - + + +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 5.1 4.5 - - + -
79B PHE* 4.7 18.2 - - + -
80B GLY 4.4 3.4 - - - +
81B LYS 3.7 3.1 - - - +
82B ILE* 3.4 27.6 - - + -
115B VAL* 4.2 1.8 - - + +
116B TYR* 1.3 75.5 - - - +
118B ASP* 1.3 84.2 + - - +
119B MET* 4.1 17.7 - - + -
154B ASN 3.0 4.0 - - - +
155B LYS* 3.1 1.3 - - - +
156B VAL* 2.5 37.8 + - + +
158B ILE* 3.4 47.3 - - + -
414B PHE* 4.8 9.4 - - + -
417B LEU* 5.4 3.4 - - + -
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 3.9 3.3 - - - -
80B GLY* 3.1 22.1 + - - -
81B LYS* 3.1 42.6 + - - +
83B TYR* 3.9 9.1 + - - -
117B LEU* 1.3 86.2 - - - +
119B MET* 1.3 67.9 + - - +
120B GLU* 3.9 6.7 - - + +
154B ASN* 3.8 6.2 - - - +
155B LYS* 3.8 23.2 + - - +
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ILE* 4.8 14.8 - - + -
78B ARG 3.9 3.4 - - - -
79B PHE* 4.2 22.7 - - + +
117B LEU* 4.1 21.1 - - + +
118B ASP* 1.3 80.5 - - - +
120B GLU* 1.3 62.7 + - - +
121B LYS* 3.3 4.2 + - - +
153B GLY* 3.8 8.7 - - - -
154B ASN 3.9 8.8 + - - +
156B VAL* 3.7 22.0 - - + -
417B LEU* 5.4 1.8 - - + -
421B ILE* 3.4 39.7 - - + -
437B LEU* 3.5 34.9 - - + +
441B VAL* 3.6 21.3 - - + -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLU 3.7 1.2 - - - +
77B ILE* 3.7 0.8 - - - -
78B ARG* 2.9 55.2 + - + +
79B PHE 5.6 1.8 - - - -
80B GLY* 5.7 1.1 - - - +
118B ASP* 3.9 4.9 - - + +
119B MET* 1.3 69.6 - - - +
121B LYS* 1.3 69.9 + - - +
122B SER* 5.0 3.7 + - - -
153B GLY* 4.8 12.0 - - - +
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TYR* 4.1 22.6 - - + -
76B GLU 3.8 3.4 - - - +
77B ILE* 4.5 16.4 - - + +
119B MET 3.3 8.2 + - - +
120B GLU* 1.3 83.4 - - - +
122B SER* 1.3 71.4 + - - +
123B MET* 5.8 1.1 - - - -
153B GLY* 5.3 4.4 - - - -
434B ASP* 3.6 24.5 + - - +
435B PHE* 3.0 57.7 + - + +
437B LEU* 4.3 12.8 - - + -
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TYR* 3.5 1.2 - - - +
76B GLU* 2.9 54.5 + - - -
78B ARG* 5.8 1.7 - - - +
120B GLU* 5.0 3.4 + - - -
121B LYS* 1.3 82.7 - - - +
123B MET* 1.3 76.2 + - - +
124B PHE 4.3 0.2 - - - -
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Residues in contact with MET 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 6.5 1.1 - - + -
72B ASN 4.3 0.2 - - - +
73B LYS* 3.6 9.2 - - + -
74B ARG 3.2 33.2 - - - +
75B TYR* 3.2 47.6 - - + +
76B GLU* 5.6 0.4 - - - -
121B LYS* 5.8 1.6 - - - -
122B SER* 1.3 91.0 - - - +
124B PHE* 1.3 68.4 + - - +
125B THR* 3.5 12.7 + - + +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG* 4.9 4.0 - - - -
57B ILE* 5.3 11.0 - - + -
71B ILE* 5.5 0.5 - - - +
72B ASN 2.8 23.9 - - - +
74B ARG* 2.9 59.8 + - + -
76B GLU* 3.2 44.2 + - + -
122B SER* 4.3 0.4 + - - -
123B MET* 1.3 77.9 - - - +
125B THR* 1.3 62.6 + - - +
126B SER* 3.5 16.6 - - - +
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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