Contacts of the strand formed by residues 114 - 124 (chain B) in PDB entry 1PU5
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 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B SER* 3.2 3.4 - - - -
43B THR* 3.1 32.4 + - - +
112B LYS* 3.5 1.4 + - - -
113B GLU* 1.3 76.7 - - - +
115B THR* 1.3 64.0 + - - -
116B TYR* 3.8 12.5 - - - -
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Residues in contact with THR 115 (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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20B ARG* 5.6 1.1 + - + -
40B VAL* 4.0 13.5 - - + -
41B GLY 3.3 9.9 - - - +
42B SER* 3.6 15.1 - - - -
114B GLY* 1.3 74.7 - - - -
116B TYR* 1.3 68.9 + - - +
117B SER* 3.9 17.2 + - - +
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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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39B VAL* 3.9 1.0 - - - +
40B VAL* 3.3 5.0 - - - +
41B GLY* 2.8 42.1 + - - +
42B SER* 5.1 1.3 - - - -
43B THR* 4.5 8.5 - - + -
47B LEU* 6.3 0.2 - - + -
105B LEU* 4.0 14.4 - - + -
106B PRO* 3.8 36.6 - - + +
111B PHE* 3.7 11.8 - + + -
112B LYS* 2.4 57.4 + - + +
113B GLU 5.0 0.2 - - - -
114B GLY* 3.8 20.2 - - - -
115B THR* 1.3 78.5 - - - +
117B SER* 1.3 63.1 + - - +
118B LEU 4.3 0.2 - - - -
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL 3.7 3.1 - - - -
40B VAL* 3.9 22.2 - - - +
103B TYR* 4.3 5.0 - - - +
105B LEU* 3.5 21.5 - - - +
115B THR* 3.9 9.4 + - - +
116B TYR* 1.3 78.7 + - - +
118B LEU* 1.3 60.0 + - - +
119B PRO* 3.6 10.7 - - - +
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Residues in contact with LEU 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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37B LEU* 3.8 29.4 - - + +
38B SER* 3.2 3.3 - - - -
39B VAL* 2.9 45.9 + - + +
40B VAL* 5.0 1.4 - - - +
99B PRO* 3.8 17.0 - - + +
100B LEU* 4.7 9.6 - - + -
103B TYR* 3.8 17.0 - - + -
105B LEU* 3.8 17.9 - - + -
116B TYR 4.3 0.2 - - - -
117B SER* 1.3 73.4 - - - +
119B PRO* 1.3 69.5 - - - +
121B SER* 3.7 16.8 - - - +
123B PHE* 4.3 17.7 - - + -
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Residues in contact with PRO 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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37B LEU 3.6 0.5 - - - +
38B SER* 3.9 1.8 - - - -
103B TYR* 3.5 47.3 - - + +
117B SER* 3.6 12.8 - - - +
118B LEU* 1.3 94.4 - - - +
120B LYS* 1.3 58.4 + - - +
121B SER* 2.7 25.5 + - - -
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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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23B THR* 4.1 18.5 - - - +
25B GLU* 3.0 36.0 + - - +
36B THR* 3.7 17.0 - - + -
37B LEU 3.4 7.0 - - - -
38B SER* 3.6 18.7 - - - +
103B TYR* 5.1 2.9 + - - -
119B PRO* 1.3 73.9 - - - +
121B SER* 1.3 59.4 + - - +
122B GLU* 5.5 0.2 - - - -
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Residues in contact with SER 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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36B THR* 3.3 2.1 - - - +
37B LEU 2.9 30.7 + - - +
99B PRO* 3.7 30.1 - - - +
103B TYR* 4.0 8.3 + - - -
118B LEU* 3.7 12.1 - - - +
119B PRO 2.7 19.1 + - - -
120B LYS* 1.3 74.2 + - - +
122B GLU* 1.3 68.9 + - - +
123B PHE* 3.5 12.2 - - - -
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Residues in contact with GLU 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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34B ASN* 4.6 18.8 - - + +
35B VAL 3.4 8.5 - - - +
36B THR* 2.4 38.4 + - - +
99B PRO* 5.2 3.3 - - - +
120B LYS 5.5 0.2 - - - -
121B SER* 1.3 75.6 - - - +
123B PHE* 1.3 70.7 + - - +
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Residues in contact with PHE 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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34B ASN* 3.3 5.5 - - - -
35B VAL* 2.9 48.7 + - + +
37B LEU* 4.2 27.1 - - + -
98B GLU 4.8 1.8 - - - -
99B PRO* 3.6 37.5 - - + -
100B LEU* 5.3 4.7 - - + -
118B LEU* 4.3 10.1 - - + -
121B SER* 3.5 25.8 - - - -
122B GLU* 1.3 77.7 - - - +
124B VAL* 1.3 68.7 + - - +
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Residues in contact with VAL 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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33B GLY 4.5 2.9 - - - +
34B ASN* 3.4 20.9 - - - +
123B PHE* 1.3 77.7 - - - +
125B VAL* 1.3 74.2 + - - +
126B PRO* 3.3 13.3 - - + +
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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