Contacts of the strand formed by residues 38 - 48 (chain D) in PDB entry 1EJH
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 PRO 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D ILE* 5.6 1.1 - - + -
36D LYS 3.0 12.9 - - - +
37D HIS* 1.3 83.5 - - - +
39D LEU* 1.3 66.2 + - - +
67D ASP* 3.7 7.9 - - - +
68D THR* 4.4 5.4 - - + -
624H TYR* 3.1 27.7 + - - +
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PRO* 1.3 81.0 - - - +
40D GLN* 1.3 65.7 + - - +
41D ASN* 3.2 17.9 + - - +
43D TRP* 4.2 1.8 - - + +
66D PHE* 3.9 23.6 - - + -
67D ASP* 2.8 26.9 + - - +
68D THR 3.6 21.8 - - - +
69D VAL* 3.6 31.6 - - + +
72D PHE* 5.0 0.2 - - + -
138D ILE* 3.7 38.8 - - + +
624H TYR* 4.7 7.4 - - + -
629H LEU* 5.1 0.9 - - + -
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Residues in contact with GLN 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 1.3 75.0 - - - +
41D ASN* 1.3 75.7 + - - +
138D ILE 4.7 3.8 + - - -
140D GLU* 3.5 34.5 - - + +
147D ASP* 5.9 2.9 - - - +
624H TYR* 5.6 2.2 - - - -
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Residues in contact with ASN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 3.2 16.9 - - - +
40D GLN* 1.3 96.4 + - - +
42D ARG* 1.3 65.1 + - - +
43D TRP* 3.1 36.0 + - + +
67D ASP* 4.1 4.0 - - - -
95D LYS* 3.9 33.7 + - + +
140D GLU* 3.5 16.6 + - - +
147D ASP* 5.5 2.6 + - - +
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASN* 1.3 76.7 - - - +
43D TRP* 1.3 65.8 + - - +
65D LYS* 4.5 11.2 - - + -
66D PHE 3.3 19.3 - - - +
67D ASP* 3.6 30.7 + - + +
95D LYS* 3.7 4.0 - - - -
96D ASP* 2.8 58.0 + - + +
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Residues in contact with TRP 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LEU* 4.2 3.5 - - + +
41D ASN* 3.1 40.0 + - + +
42D ARG* 1.3 77.1 - - - +
44D ALA* 1.3 62.6 + - - +
45D LEU 4.3 0.2 - - - -
64D SER 4.0 0.4 - - - +
65D LYS* 3.1 8.4 - - - +
66D PHE* 2.8 55.0 + + + -
93D LEU* 3.8 20.0 - - + -
94D PHE 3.5 22.7 - - - -
95D LYS* 3.6 37.5 - - + -
96D ASP* 4.6 1.3 - - - -
137D LEU* 3.2 53.8 - - + -
138D ILE* 3.7 30.1 + - + +
140D GLU* 3.7 10.4 + - - -
149D VAL* 4.5 4.9 - - + -
150D CYS 4.0 4.0 - - - -
151D GLY* 4.2 1.1 - - - -
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Residues in contact with ALA 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D TRP* 1.3 76.4 - - - +
45D LEU* 1.3 60.3 + - - +
46D TRP* 3.3 21.5 - - + +
62D LEU* 3.6 20.4 - - + -
64D SER 3.4 4.7 - - - -
65D LYS* 3.8 17.9 - - + -
92D SER 3.3 1.2 - - - +
93D LEU* 3.4 4.6 - - - -
94D PHE 2.9 32.1 + - - +
95D LYS 5.4 0.2 - - - +
96D ASP* 4.9 7.4 - - - -
97D GLY 5.9 0.4 - - - +
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ALA* 1.3 72.8 - - - +
46D TRP* 1.3 56.1 + - - +
62D LEU* 3.2 4.9 - - - +
63D ILE* 2.7 47.7 + - + +
64D SER 2.9 8.6 + - - +
66D PHE* 5.0 0.4 - - - -
75D LEU* 3.7 35.2 - - + -
79D ILE* 3.3 33.4 - - + -
91D TYR* 4.0 23.8 - - + -
92D SER 3.2 19.1 - - - +
93D LEU* 4.0 15.8 - - + +
130D TRP* 5.1 6.1 - - + +
134D LEU* 5.8 2.5 - - + -
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Residues in contact with TRP 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LYS 4.5 3.1 - - - -
55B THR* 3.9 28.5 - - + -
44D ALA* 3.3 31.3 + - + +
45D LEU* 1.3 75.8 - - - +
47D PHE* 1.3 60.7 + - - +
60D LEU* 4.1 14.6 - - + -
61D ARG 3.3 8.7 - - - +
62D LEU* 3.7 48.7 - - + -
63D ILE* 4.7 0.4 - - - -
65D LYS* 5.8 1.6 - - - -
90D ASP 3.9 0.2 - - - +
91D TYR* 3.4 10.3 - - - -
92D SER* 2.7 47.8 + - - +
94D PHE* 4.6 5.4 - - + +
98D ILE 4.1 9.2 + - - -
99D GLU* 4.3 27.1 - - + -
100D PRO* 3.6 34.8 - - + +
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Residues in contact with PHE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D TRP* 1.3 74.7 - - - +
48D PHE* 1.3 79.9 + - - +
49D LYS* 4.1 16.6 - - + -
59D ASN 3.6 2.6 - - - +
60D LEU* 3.7 4.1 - - - +
61D ARG* 2.7 43.3 + - + +
63D ILE* 3.4 29.6 - - + +
85D LEU* 3.6 28.5 - - + -
89D CYS* 3.7 21.5 - - + -
90D ASP 3.3 12.6 - - - -
91D TYR* 3.8 15.0 - + + -
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Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D PHE* 1.3 80.8 - - - +
49D LYS* 1.3 74.5 + - - +
50D ASN* 4.1 12.3 - - - -
56D TRP* 3.6 44.2 - + - -
59D ASN* 3.5 31.2 - - + -
60D LEU* 4.1 22.2 - - + -
88D GLY 3.4 24.5 - - - -
89D CYS* 3.1 27.5 - - - +
90D ASP* 2.8 41.3 + - + +
157D ARG* 5.3 2.2 - - - -
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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