Contacts of the strand formed by residues 142 - 148 (chain S) in PDB entry 5IY8
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 ASN 142 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27S ASN* 3.2 21.8 + - - +
28S ILE 3.2 20.6 + - - -
114S LYS* 3.4 34.0 + - - +
115S LYS* 4.4 5.4 - - - +
140S VAL* 3.4 13.6 - - - +
141S HIS* 1.3 93.9 + - + +
143S TRP* 1.3 71.1 + - - +
144S TYR* 2.6 40.7 + - + +
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Residues in contact with TRP 143 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B GLU* 4.5 18.8 + - + -
555B GLU* 4.5 24.2 - - + -
28S ILE* 3.7 28.2 - - + +
30S ALA* 3.7 13.0 - - + +
114S LYS* 3.6 1.7 - - - -
115S LYS* 2.7 64.9 + - + +
124S TYR* 4.9 20.4 - + + -
140S VAL* 5.4 4.0 - - + -
142S ASN* 1.3 80.3 + - - +
144S TYR* 1.3 81.2 + - - +
145S ASN* 4.1 7.5 + - + +
20T LEU* 4.2 19.1 - - + -
91T GLN* 5.5 0.9 - - - -
93T LEU* 3.8 40.4 - - + -
113T ARG* 5.1 2.7 - - - -
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Residues in contact with TYR 144 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S ASN* 3.7 17.3 - - + -
28S ILE 2.9 23.9 + - - +
29S MET* 3.9 1.9 - - - -
30S ALA 3.7 10.4 + - - -
49S ARG* 3.8 21.0 + - - -
94S GLU 4.7 4.5 + - - -
96S GLN 4.9 2.7 - - - -
97S PRO* 5.8 0.9 - - + -
98S TRP* 3.1 46.4 - + + -
112S GLY 4.9 0.9 - - - -
113S ILE 3.2 4.3 - - - +
114S LYS* 3.8 27.8 - - + -
141S HIS* 5.2 3.3 - + - -
142S ASN* 2.6 42.4 + - + +
143S TRP* 1.3 83.9 - - - +
145S ASN* 1.3 60.2 + - - +
146S PHE* 3.9 10.7 - - + -
96T PHE* 3.7 13.9 - + - -
98T GLU* 5.2 0.9 + - - -
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Residues in contact with ASN 145 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B PHE* 6.3 0.8 - - - -
359B THR* 6.1 3.6 - - + +
554B GLU 5.1 5.7 - - - +
30S ALA* 4.2 17.1 - - - +
111S LYS 2.9 5.9 - - - +
112S GLY* 3.1 0.3 - - - -
113S ILE* 2.7 49.7 + - + +
143S TRP* 4.1 8.1 + - + +
144S TYR* 1.3 73.7 - - - +
146S PHE* 1.3 63.5 + - - +
147S THR* 3.2 32.4 + - - +
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Residues in contact with PHE 146 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S MET* 3.6 35.4 - - + -
30S ALA 3.3 16.6 + - - +
31S PHE* 3.4 30.3 - - + -
32S ASN 5.5 0.5 + - - -
47S LEU* 3.9 15.7 - - + -
98S TRP* 3.9 27.6 - + + -
100S LEU* 3.5 37.9 - - + -
110S PHE* 4.0 10.3 - - + -
111S LYS 3.1 3.1 - - - -
112S GLY* 4.0 8.7 - - - -
144S TYR* 3.9 25.4 - - + -
145S ASN* 1.3 78.0 + - - +
147S THR* 1.3 65.5 + - - +
148S PRO* 4.7 1.2 - - - +
96T PHE* 4.1 10.3 - + - -
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Residues in contact with THR 147 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B PHE* 5.7 10.7 - - + -
283B ASP* 5.7 4.9 - - - +
110S PHE* 3.2 9.0 - - - +
111S LYS* 3.0 36.5 + - - +
113S ILE* 5.4 4.6 - - + +
145S ASN* 3.2 28.0 - - - +
146S PHE* 1.3 74.3 - - - +
148S PRO* 1.4 77.7 + - + +
149S LEU* 3.1 5.0 + - - +
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Residues in contact with PRO 148 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B VAL* 4.7 13.0 - - - +
280B SER* 4.8 13.5 + - - +
283B ASP* 5.3 7.4 - - - +
21I ASN* 6.0 5.6 - - + +
35S ASP* 3.5 15.7 - - + +
108S ARG* 3.5 25.1 - - - +
110S PHE* 3.7 12.5 - - + -
146S PHE 4.7 0.4 - - - +
147S THR* 1.4 90.7 + - + +
149S LEU* 1.3 67.9 + - - +
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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