Contacts of the strand formed by residues 26 - 33 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H VAL* 4.7 6.1 - - + +
23H LEU* 3.0 10.2 + - - +
24H PRO* 3.8 3.5 - - - +
25H ALA* 1.4 79.5 - - + +
27H VAL* 1.3 69.2 + - - +
67H GLY 3.4 12.8 - - - +
68H VAL* 4.6 3.6 - - + +
95H ASN 4.8 7.1 + - - -
127H ILE* 5.3 3.6 - - + -
144H VAL* 3.6 44.4 - - + +
145H GLY* 4.4 4.9 - - - +
152H GLN* 3.0 28.1 - - + +
189H GLY* 4.6 1.8 - - - -
190H ALA* 3.7 28.3 - - + +
192H LEU* 5.2 5.2 - - + -
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Residues in contact with VAL 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H PRO 4.3 0.9 - - - +
25H ALA 3.8 1.3 - - - +
26H VAL* 1.3 81.8 - - - +
28H SER* 1.3 59.1 + - - +
29H VAL* 4.0 3.4 - - + -
66H SER* 3.1 9.4 - - - -
67H GLY* 2.8 51.4 + - - +
69H ILE* 3.6 34.1 - - + -
77H VAL* 3.9 8.7 - - + -
92H ILE* 3.9 29.8 - - + -
93H GLN 3.6 11.0 - - - +
94H LEU* 3.7 17.5 - - + -
146H ASN* 5.4 0.4 - - - -
152H GLN* 6.5 0.4 - - - -
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Residues in contact with SER 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H VAL* 1.3 74.3 - - - +
29H VAL* 1.3 63.3 + - - +
30H ARG* 4.0 2.9 + - - +
64H LEU* 3.4 24.3 - - - +
65H GLY 3.6 4.9 - - - -
66H SER* 4.4 0.2 - - - +
91H SER 3.9 0.2 - - - +
92H ILE* 3.4 5.2 - - - -
93H GLN* 2.9 55.8 + - - +
146H ASN* 3.3 22.5 + - - -
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Residues in contact with VAL 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H VAL* 4.0 7.0 - - + -
28H SER* 1.3 77.2 + - - +
30H ARG* 1.3 60.5 + - - +
31H VAL* 4.0 3.9 + - + +
63H GLY 3.9 0.3 - - - +
64H LEU* 3.5 5.8 - - - -
65H GLY 2.8 37.4 + - - +
66H SER 3.4 29.2 - - - +
67H GLY* 3.9 5.6 - - - +
77H VAL* 4.7 1.1 - - + -
79H THR* 4.6 0.9 - - - +
83H VAL* 3.9 10.6 - - + +
84H ILE* 3.7 29.8 - - + -
90H ILE* 4.2 14.1 - - + -
91H SER 3.6 2.5 - - - -
92H ILE* 3.9 15.5 - - + -
116H LEU* 4.4 6.7 - - + -
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Residues in contact with ARG 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H SER* 4.0 3.9 - - - +
29H VAL* 1.3 72.7 - - - +
31H VAL* 1.3 66.5 + - - +
32H GLU* 5.2 9.4 + - + +
62H GLU* 3.1 35.7 + - + +
63H GLY 3.6 7.6 - - - +
64H LEU* 4.4 18.6 - - + +
89H LYS 4.0 0.3 - - - +
90H ILE* 3.4 4.2 - - - +
91H SER* 2.8 55.5 + - - +
93H GLN* 6.4 2.0 - - + -
99H GLU* 5.7 5.3 + - - -
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Residues in contact with VAL 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H VAL* 4.3 6.5 - - + +
30H ARG* 1.3 79.8 - - - +
32H GLU* 1.3 66.7 + - - +
61H PHE* 3.7 24.0 - - + -
62H GLU* 3.3 6.2 - - - +
63H GLY* 2.8 40.2 + - - +
83H VAL* 3.7 26.5 - - + +
84H ILE* 3.9 11.9 - - + -
86H GLN 5.8 0.2 - - - +
87H ALA* 3.6 32.5 - - + +
89H LYS 3.4 2.7 - - - -
90H ILE* 3.9 12.3 - - + -
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Residues in contact with GLU 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ARG* 5.2 11.1 + - + +
31H VAL* 1.3 81.5 - - - +
33H GLY* 1.3 52.3 + - - +
61H PHE 3.4 5.8 - - - +
62H GLU* 3.2 33.8 - - + +
87H ALA 3.7 0.2 - - - -
88H GLN* 2.7 31.1 + - - +
89H LYS* 2.9 44.5 + - + +
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Residues in contact with GLY 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H GLU* 1.3 76.0 - - - +
34H THR* 1.3 58.6 + - - -
60H PRO* 3.3 23.9 - - - +
61H PHE* 3.2 26.7 + - - +
86H GLN 3.7 9.4 - - - -
88H 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