Contacts of the strand formed by residues 115 - 123 (chain B) in PDB entry 4PBY
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 ILE 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B MET* 4.0 31.4 - - + -
37B THR 4.6 4.9 - - - +
38B HIS* 3.5 59.5 + - + +
40B LEU* 6.0 1.1 - - + -
82B ALA* 4.9 6.3 - - + -
83B SER 3.2 10.3 - - - +
84B VAL* 4.2 11.4 - - + -
113B GLY 3.8 2.6 + - - +
114B LYS* 1.3 77.4 - - - +
116B GLU* 1.3 63.7 + - - +
117B ILE* 4.0 3.6 + - + +
399B MET* 3.8 30.3 - - + -
401B VAL* 5.1 3.4 - - + -
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Residues in contact with GLU 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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82B ALA* 3.3 4.9 - - - +
83B SER* 2.7 51.1 + - - +
85B GLN* 5.7 1.9 + - - -
114B LYS* 3.5 40.3 + - - +
115B ILE* 1.3 75.9 - - - +
117B ILE* 1.3 66.2 + - - +
118B GLU* 5.0 4.0 - - + -
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Residues in contact with ILE 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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38B HIS* 5.0 13.7 - - + -
40B LEU* 5.4 10.1 - - + -
41B GLU* 6.2 3.6 - - + +
80B VAL* 4.2 15.7 - - + -
81B ILE 4.0 6.3 - - - +
82B ALA* 4.3 4.9 - - + +
115B ILE* 4.8 6.3 - - + +
116B GLU* 1.3 78.8 - - - +
118B GLU* 1.3 61.8 + - - +
119B ILE 3.6 22.4 - - - +
120B LYS* 4.0 27.6 - - + -
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Residues in contact with GLU 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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63B ILE* 5.2 4.7 - - - +
65B ARG* 4.1 22.8 + - - -
81B ILE* 3.0 12.9 + - + +
82B ALA 4.8 0.2 - - - -
83B SER* 3.5 34.8 + - - +
116B GLU* 3.8 4.2 + - + -
117B ILE* 1.3 75.5 - - - +
119B ILE* 1.3 78.4 + - + +
159B SER* 3.8 13.2 + - - +
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Residues in contact with ILE 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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65B ARG* 6.1 0.2 - - - +
79B LEU 4.5 2.0 - - - +
80B VAL* 3.5 2.6 - - - -
81B ILE* 3.3 50.0 + - + +
117B ILE* 3.6 6.6 - - - +
118B GLU* 1.3 93.3 - - + +
120B LYS* 1.3 72.9 - - - +
121B ILE* 3.8 30.7 - - + -
154B TYR* 4.6 22.2 - - + +
158B PRO 4.6 4.3 - - - +
159B SER* 3.7 28.0 - - - +
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Residues in contact with LYS 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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41B GLU* 3.8 21.8 + - - -
78B HIS* 4.1 29.2 - - + +
79B LEU 3.5 4.5 - - - -
80B VAL* 4.4 13.0 - - + -
117B ILE* 4.0 23.6 - - + -
119B ILE* 1.3 80.7 - - - +
121B ILE* 1.3 66.2 - - - +
158B PRO 4.3 3.1 - - - +
159B SER 3.9 5.1 + - - -
160B LYS 4.2 2.9 - - - -
161B PRO* 3.8 40.4 - - + +
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Residues in contact with ILE 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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78B HIS* 3.1 9.2 - - - +
79B LEU* 2.7 59.7 + - + +
81B ILE* 6.3 0.7 - - + -
119B ILE* 3.8 15.3 - - + -
120B LYS* 1.3 80.1 - - - +
122B ASN* 1.3 76.0 - - + +
123B HIS* 4.0 0.2 - - - +
152B PHE* 4.3 15.7 - - + -
154B TYR* 3.6 36.1 - - + +
157B HIS* 3.8 41.3 - - + +
158B PRO 4.6 2.5 - - - +
161B PRO* 5.0 0.4 - - - -
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Residues in contact with ASN 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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76B GLN* 4.2 5.3 - - - +
77B ASN 4.0 3.4 - - - -
78B HIS* 3.3 22.5 - - - -
121B ILE* 1.3 84.4 - - - +
123B HIS* 1.3 58.0 + - - +
152B PHE* 3.9 4.5 - - - -
161B PRO* 3.4 14.3 - - - +
162B ASP* 3.1 30.8 + - - +
165B GLY* 3.4 8.5 - - - -
166B GLU 3.0 44.6 + - - +
167B CYS* 3.3 18.0 - - - -
168B ASN 4.4 1.5 + - - +
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Residues in contact with HIS 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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76B GLN* 3.0 19.0 + - - +
77B ASN* 3.0 19.9 + - - +
78B HIS* 4.1 2.0 - - - -
79B LEU* 3.9 18.6 - - + +
122B ASN* 1.3 75.4 - - - +
124B GLU* 1.3 59.9 + - - +
125B GLY 2.5 39.0 + - - -
126B GLU 3.4 8.5 - - - -
127B VAL* 3.4 28.2 - - + +
142B THR* 3.0 31.2 + - + -
144B THR* 3.3 25.2 - - + +
150B LEU* 4.1 3.6 - - + -
152B PHE* 3.9 18.8 - + - -
167B CYS* 3.6 4.9 - - - -
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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