Contacts of the strand formed by residues 22 - 30 (chain A) in PDB entry 4PSQ
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A SER* 1.3 76.4 - - - +
23A THR* 1.3 62.7 + - - -
24A TRP* 3.8 4.5 + - - -
43A ALA 3.8 0.9 - - - +
44A GLU* 3.2 14.6 - - - -
45A PHE* 2.8 34.0 + - - -
139A ARG* 3.5 4.5 - - - -
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Residues in contact with THR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY* 1.3 71.9 - - - -
24A TRP* 1.3 62.4 + - - +
25A TYR* 3.9 27.1 - - + +
42A VAL* 3.8 22.2 - - + -
43A ALA 3.6 2.5 - - - -
44A GLU* 2.7 31.2 + - - +
139A ARG* 2.9 33.2 + - - +
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Residues in contact with TRP 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 2.8 55.3 + + - -
22A GLY 3.9 6.3 - - - -
23A THR* 1.3 72.7 - - - +
25A TYR* 1.3 62.4 + - - +
26A ALA 4.0 0.5 + - - -
42A VAL* 3.6 4.9 - - - +
43A ALA* 2.9 37.7 + - + +
45A PHE* 3.8 22.0 - + - -
109A THR* 3.7 4.7 - - - -
111A TYR 3.7 11.9 - - - -
114A TYR* 3.2 42.6 - - - -
115A ALA* 3.7 1.3 - - + -
137A PHE* 3.5 36.5 - + + -
138A SER 3.8 14.4 - - - -
139A ARG* 3.3 46.9 - - + -
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Residues in contact with TYR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A THR* 3.9 24.4 - - + +
24A TRP* 1.3 73.3 - - - +
26A ALA* 1.3 62.5 + - - +
27A MET* 3.4 6.4 + - + +
41A ILE 4.1 2.7 - - - -
42A VAL* 3.9 19.3 - - + -
137A PHE* 3.3 2.3 - - - -
138A SER* 2.8 41.9 + - - +
139A ARG 3.5 27.1 - - - -
141A PRO* 3.7 39.7 - - + +
170A HIS* 3.8 28.9 - + + +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TRP 4.0 0.2 + - - -
25A TYR* 1.3 70.3 - - - +
27A MET* 1.3 60.8 + - - +
41A ILE* 3.1 34.5 + - + +
135A PHE* 4.0 10.3 - - + -
136A VAL 3.5 7.4 - - - +
137A PHE* 3.8 17.8 - - + -
168A ILE* 3.6 28.8 - - + +
170A HIS* 3.0 19.2 + - - -
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Residues in contact with MET 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 3.8 15.5 - - + +
26A ALA* 1.3 76.2 - - - +
28A ALA* 1.3 61.5 + - + +
136A VAL* 2.9 15.1 + - + +
138A SER* 3.6 24.0 - - - -
140A ASP 3.7 12.1 - - - +
141A PRO* 3.8 15.7 - - + +
142A ASN 4.6 1.3 - - - +
143A GLY* 3.8 24.0 - - - +
144A LEU* 4.9 5.4 - - + +
167A LEU* 3.4 13.5 - - + +
168A ILE* 2.8 30.6 + - - +
170A HIS* 5.1 4.9 - - + -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA 3.7 0.4 - - - -
27A MET* 1.3 79.4 - - + +
29A LYS* 1.3 64.2 + - - +
135A PHE* 3.7 2.3 - - - -
136A VAL* 2.9 46.9 + - + +
156A GLN* 5.0 2.5 - - - +
165A TYR* 4.3 11.9 - - + -
166A ARG 3.3 13.5 - - - +
167A LEU* 4.2 14.4 - - + -
168A ILE* 3.6 7.3 - - - +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 1.3 77.8 - - - +
30A LYS* 1.3 60.6 + - - +
31A ASP* 2.7 36.1 + - - +
36A PHE* 4.1 7.6 - - + -
37A LEU 3.4 15.3 + - - +
38A GLN* 3.1 35.1 + - - +
41A ILE* 4.1 3.4 - - + -
134A SER 3.2 13.2 - - - +
135A PHE* 3.8 20.9 - - + -
165A TYR* 3.6 7.6 - - - -
166A ARG* 2.9 47.3 + - + +
168A ILE* 3.6 20.9 - - + -
212A EDO 3.6 5.0 - - - -
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 1.3 74.9 - - - +
31A ASP* 1.3 73.9 + - - +
32A PRO* 4.4 1.0 - - - +
36A PHE* 4.9 1.2 - - - -
131A ASP* 5.2 1.6 + - - +
132A SER* 2.7 44.7 + - - +
133A TYR* 3.2 11.1 - - - +
134A SER 3.0 28.4 + - - +
161A LEU* 3.6 19.1 - - + -
164A GLN* 3.4 49.4 - - + +
165A TYR* 3.6 19.9 - - + -
209A EDO 4.5 6.3 + - - -
212A EDO 3.4 5.8 - - - +
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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