Contacts of the strand formed by residues 35 - 42 (chain B) in PDB entry 2JAM
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 SER 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B SER* 4.4 0.3 + - - -
32B GLY* 2.7 34.2 + - - +
33B ALA 3.8 0.4 + - - -
34B PHE* 1.3 84.9 + - - +
36B GLU* 1.3 58.5 + - - +
52B LYS* 4.4 5.2 - - - -
53B CYS 3.1 12.3 - - - -
54B ILE* 4.2 15.0 - - - -
169B SER* 2.8 30.1 + - - -
170B LYS 4.2 1.4 + - - -
171B MET* 3.4 16.8 - - - +
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 5.4 3.9 - - + +
30B GLY 3.4 12.6 - - - +
31B SER* 4.3 11.6 + - - +
35B SER* 1.3 77.9 - - - +
37B VAL* 1.3 64.2 + - - +
38B PHE* 3.5 36.5 - - + -
51B LEU 3.6 0.5 - - - +
52B LYS* 3.4 3.1 - - - +
53B CYS* 2.8 48.2 + - + +
93B HIS* 5.8 2.9 + - - -
171B MET* 3.8 2.7 - - - -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.7 4.2 - - - +
29B LEU* 2.7 42.8 + - + -
30B GLY 2.9 15.4 + - - +
36B GLU* 1.3 80.5 - - - +
38B PHE* 1.3 60.2 + - - +
50B ALA* 4.0 27.8 - - + -
51B LEU 3.3 8.3 - - - +
52B LYS* 3.8 14.4 - - + +
171B MET* 3.6 20.9 - - + -
1305B J60 3.5 36.6 - - + -
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Residues in contact with PHE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PHE* 3.7 29.4 - + + -
27B GLU 3.3 11.0 - - - +
28B VAL* 3.7 31.9 - - + -
29B LEU* 4.1 4.9 - - - -
36B GLU* 3.5 45.5 - - + -
37B VAL* 1.3 75.1 - - - +
39B LEU* 1.3 63.1 + - - +
40B VAL* 3.5 18.3 + - + +
50B ALA* 3.5 4.2 - - - -
51B LEU* 2.9 31.6 + - - +
53B CYS* 3.8 23.1 - - - -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B MET* 2.8 48.0 + - + +
27B GLU* 2.8 49.1 + - + +
29B LEU* 3.7 16.2 - - + +
38B PHE* 1.3 70.7 - - - +
40B VAL* 1.3 70.3 + - - +
48B LEU* 4.4 11.7 - - + -
49B PHE 3.7 6.3 - - - +
100B LEU* 3.5 37.0 - - + -
1305B J60 6.5 0.4 - - + -
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.5 32.1 - - + -
24B ILE 3.2 10.5 - - - +
25B PHE* 3.9 29.6 - - + -
26B MET* 4.4 1.8 - - - -
38B PHE* 3.9 3.1 - - + -
39B LEU* 1.3 80.3 - - - +
41B LYS* 1.3 60.3 + - - +
47B LYS 4.0 0.2 - - - +
48B LEU* 3.3 10.3 - - - +
49B PHE* 3.0 49.0 + - + +
51B LEU* 3.8 33.9 - - + -
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 3.4 4.1 - - - -
24B ILE* 2.8 52.7 + - + +
26B MET* 3.6 31.4 - - + -
40B VAL* 1.3 73.5 - - - +
42B GLN* 1.3 69.4 - - - +
43B ARG* 3.3 1.7 + - - -
46B GLY* 3.1 42.4 - - - +
47B LYS 3.4 3.6 - - - -
48B LEU* 3.7 7.0 - - + -
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B THR* 3.7 15.6 - - + +
23B PHE* 3.6 27.7 - - + -
40B VAL 4.2 0.2 - - - -
41B LYS* 1.3 70.2 - - - +
43B ARG* 1.3 59.3 + - - +
44B LEU* 4.1 20.1 - - + +
45B THR* 2.8 36.2 + - - +
46B GLY* 2.7 34.8 + - - -
47B LYS* 2.9 13.8 + - - +
49B PHE* 3.8 18.1 - - + -
88B TYR* 5.8 1.6 + - - -
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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