Contacts of the strand formed by residues 26 - 33 (chain A) in PDB entry 3STJ
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 VAL 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A VAL 4.3 8.7 - - - +
23A LEU* 3.1 9.9 + - - +
24A PRO 3.9 3.3 - - - +
25A ALA* 1.3 80.7 - - + +
27A VAL* 1.3 64.1 - - - +
67A GLY 3.4 15.3 - - - +
68A VAL* 4.5 5.6 - - + +
95A ASN 4.8 6.4 + - - -
127A ILE* 5.1 3.4 - - + -
144A VAL* 3.6 42.2 - - + +
145A GLY* 4.6 3.1 - - - +
152A GLN* 2.9 29.3 - - + +
189A GLY* 4.5 2.2 - - - -
190A ALA* 3.6 29.8 - - + +
192A LEU* 5.2 4.7 - - + -
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Residues in contact with VAL 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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24A PRO 4.5 0.9 - - - +
25A ALA 4.4 0.9 - - - -
26A VAL* 1.3 80.3 - - - +
28A SER* 1.3 56.6 + - - +
29A VAL* 4.2 2.0 - - + -
66A SER* 3.3 8.7 + - - -
67A GLY* 2.8 55.2 + - - +
69A ILE* 3.6 23.8 - - + -
77A VAL* 3.9 17.0 - - + -
92A ILE* 3.9 21.8 - - + -
93A GLN 3.6 10.1 - - - +
94A LEU* 3.5 29.6 - - + -
145A GLY* 5.7 0.2 - - - -
146A ASN* 5.3 0.2 - - - -
152A GLN* 5.8 0.2 - - - -
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Residues in contact with SER 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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27A VAL* 1.3 73.0 - - - +
29A VAL* 1.3 63.6 + - - +
30A ARG* 4.0 3.2 + - - +
64A LEU* 3.7 18.5 - - - +
65A GLY 3.7 5.4 - - - -
66A SER* 4.9 0.2 - - - -
91A SER 3.8 0.5 - - - +
92A ILE* 3.3 7.4 - - - +
93A GLN* 2.9 54.1 + - - +
146A ASN* 3.3 24.0 + - - -
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Residues in contact with VAL 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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27A VAL* 4.2 1.1 - - + -
28A SER* 1.3 76.9 + - - +
30A ARG* 1.3 58.7 + - - +
31A VAL* 4.1 3.7 + - + +
63A GLY 4.0 0.5 - - - +
64A LEU* 3.5 5.4 - - - +
65A GLY 2.9 35.4 + - - +
66A SER 3.5 28.5 - - - +
67A GLY* 3.7 9.0 - - - +
77A VAL* 4.6 0.4 - - + -
79A THR* 4.4 2.0 - - - +
83A VAL* 4.0 9.7 - - + +
84A ILE* 3.7 30.1 - - + -
90A ILE* 4.0 16.2 - - + -
91A SER 3.6 2.2 - - - -
92A ILE* 3.9 17.3 - - + -
116A LEU* 4.3 8.3 - - + -
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Residues in contact with ARG 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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28A SER* 4.0 3.7 - - - +
29A VAL* 1.3 72.1 - - - +
31A VAL* 1.3 67.1 + - - +
32A GLU* 5.2 9.4 + - + +
62A GLU* 3.1 36.1 + - + +
63A GLY 3.6 8.1 - - - +
64A LEU* 4.4 19.1 - - + +
89A LYS 4.0 0.3 - - - +
90A ILE* 3.4 4.3 - - - +
91A SER* 2.8 57.0 + - - +
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Residues in contact with VAL 31 (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 VAL* 4.3 6.3 - - + +
30A ARG* 1.3 79.6 - - - +
32A GLU* 1.4 65.1 + - - +
61A PHE* 3.7 26.7 - - + -
62A GLU* 3.3 6.9 - - - +
63A GLY* 2.8 41.4 + - - +
83A VAL* 3.6 26.9 - - + +
84A ILE* 4.0 12.6 - - + -
87A ALA* 3.7 30.5 - - + +
89A LYS 3.4 2.9 - - - -
90A ILE* 3.9 11.7 - - + -
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Residues in contact with GLU 32 (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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30A ARG* 5.2 12.3 + - + +
31A VAL* 1.4 81.3 - - - +
33A GLY* 1.3 58.0 + - - +
61A PHE 3.3 6.5 - - - +
62A GLU* 3.1 33.9 - - + +
87A ALA 3.7 0.2 - - - -
88A GLN* 2.7 23.8 + - - +
89A LYS* 2.9 42.9 + - + +
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Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLU* 1.3 75.2 - - - +
34A THR* 1.4 58.8 + - - -
60A PRO* 3.3 23.7 - - - +
61A PHE* 3.2 25.4 + - - -
86A GLN 3.6 9.2 - - - -
88A GLN* 3.6 20.8 - - - +
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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