Contacts of the strand formed by residues 26 - 33 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22L VAL 4.3 7.4 - - - +
23L LEU* 3.0 13.0 + - - +
24L PRO* 4.1 3.1 - - - +
25L ALA* 1.4 80.2 - - + +
27L VAL* 1.3 65.0 + - - +
67L GLY 3.5 14.6 - - - +
68L VAL* 4.6 3.6 - - + +
95L ASN 4.9 6.6 + - - -
127L ILE* 5.3 0.7 - - + -
144L VAL* 3.5 49.4 - - + +
145L GLY* 4.6 3.4 - - - +
152L GLN* 3.1 20.9 - - + +
189L GLY* 4.6 2.5 - - - -
190L ALA* 3.9 27.6 - - + +
192L LEU* 5.1 7.0 - - + -
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Residues in contact with VAL 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L PRO 4.5 1.8 - - - +
26L VAL* 1.3 79.1 - - - +
28L SER* 1.3 56.3 + - - +
29L VAL* 4.3 1.6 - - + -
66L SER* 3.3 8.5 - - - -
67L GLY* 2.8 51.2 + - - +
68L VAL 4.4 0.2 - - - +
69L ILE* 3.6 23.8 - - + -
77L VAL* 3.9 19.3 - - + -
92L ILE* 3.9 23.3 - - + -
93L GLN 3.6 10.1 - - - +
94L LEU* 3.5 30.3 - - + -
146L ASN* 5.5 0.8 - - - +
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Residues in contact with SER 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L VAL* 1.3 71.8 - - - +
29L VAL* 1.3 62.1 + - - +
30L ARG* 4.0 3.5 + - - +
64L LEU* 3.8 17.7 - - - +
65L GLY 3.6 5.2 - - - -
66L SER* 4.4 0.4 - - - +
91L SER 3.8 0.3 - - - +
92L ILE* 3.3 8.0 - - - +
93L GLN* 2.9 54.2 + - - +
146L ASN* 3.4 25.8 + - - -
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Residues in contact with VAL 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L VAL* 4.3 1.1 - - + -
28L SER* 1.3 76.0 - - - +
30L ARG* 1.3 60.5 + - - +
31L VAL* 4.1 3.5 + - + +
63L GLY 3.9 0.7 - - - +
64L LEU* 3.5 5.4 - - - +
65L GLY 2.8 39.6 + - - +
66L SER 3.5 27.1 - - - +
67L GLY* 3.7 9.2 - - - +
77L VAL* 4.7 0.7 - - + -
79L THR* 4.3 2.9 - - - +
83L VAL* 4.0 10.6 - - + +
84L ILE* 3.7 30.3 - - + -
90L ILE* 4.0 16.4 - - + -
91L SER 3.6 2.9 - - - +
92L ILE* 4.0 15.9 - - + -
116L LEU* 4.3 7.0 - - + -
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Residues in contact with ARG 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L SER* 4.0 4.4 - - - +
29L VAL* 1.3 72.1 - - - +
31L VAL* 1.3 66.0 + - - +
32L GLU* 5.2 9.6 + - + +
62L GLU* 3.1 35.7 + - + +
63L GLY 3.6 7.6 - - - +
64L LEU* 4.4 18.4 - - + +
89L LYS 3.9 0.3 - - - +
90L ILE* 3.4 4.5 - - - +
91L SER* 2.8 57.8 + - - +
99L GLU* 6.3 1.0 - - - -
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Residues in contact with VAL 31 (chain L).
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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29L VAL* 4.3 6.5 - - + +
30L ARG* 1.3 80.3 - - - +
32L GLU* 1.3 66.4 + - - +
61L PHE* 3.7 25.1 - - + -
62L GLU* 3.3 6.1 - - - +
63L GLY* 2.8 39.2 + - - +
83L VAL* 3.7 25.8 - - + +
84L ILE* 3.9 18.8 - - + -
87L ALA* 3.7 32.3 - - + +
89L LYS 3.4 2.7 - - - -
90L ILE* 3.9 6.3 - - + -
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Residues in contact with GLU 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ARG* 5.2 10.7 + - + +
31L VAL* 1.3 81.3 - - - +
33L GLY* 1.3 51.9 + - - +
61L PHE 3.4 6.1 - - - +
62L GLU* 3.2 34.5 - - + +
87L ALA 3.7 0.2 - - - -
88L GLN* 2.7 31.5 + - - +
89L LYS* 2.9 43.1 + - + +
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Residues in contact with GLY 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L GLU* 1.3 75.4 - - - +
34L THR* 1.4 58.2 + - - -
60L PRO* 3.3 23.6 - - - +
61L PHE* 3.2 26.9 + - - +
86L GLN 3.7 9.4 - - - -
88L GLN* 3.7 19.9 - - - +
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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