Contacts of the strand formed by residues 52 - 64 (chain D) in PDB entry 4J1R
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 GLN 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D VAL* 3.3 7.1 - - - +
42D ALA 2.9 34.1 + - - +
44D PRO* 4.2 12.2 - - - +
50D ARG* 4.4 3.1 - - + +
51D PRO* 1.3 78.5 - - - +
53D GLU* 1.3 67.5 + - - +
54D VAL* 3.5 10.1 + - + +
114D TYR* 3.2 34.6 + - - -
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Residues in contact with GLU 53 (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 THR* 5.0 15.3 - - + +
40D VAL 3.3 7.4 - - - +
41D VAL* 4.4 15.9 - - + +
52D GLN* 1.3 77.6 - - - +
54D VAL* 1.3 63.1 + - - +
55D SER* 5.3 0.9 - - - +
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Residues in contact with VAL 54 (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 THR 3.9 0.3 - - - +
39D THR* 3.3 1.8 - - - -
40D VAL* 2.7 50.2 + - + +
42D ALA* 4.1 16.6 - - + -
52D GLN* 3.7 23.6 - - + +
53D GLU* 1.3 79.6 - - - +
55D SER* 1.3 67.0 + - - +
56D TYR* 4.7 3.3 - - + -
75D LEU* 4.2 18.8 - - + -
77D ASP* 5.0 5.4 - - - +
114D TYR* 4.1 34.8 - - + -
131D VAL* 6.4 1.1 - - + -
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Residues in contact with SER 55 (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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37D VAL* 4.1 5.8 - - - -
38D THR 3.2 6.1 - - - -
39D THR* 2.7 28.4 - - - +
53D GLU* 5.3 1.0 - - - +
54D VAL* 1.3 76.3 + - - +
56D TYR* 1.3 64.5 + - - +
75D LEU* 3.5 7.3 - - - +
76D CYS* 3.0 40.6 + - - -
77D ASP* 3.7 8.3 + - - +
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Residues in contact with TYR 56 (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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36D LYS 4.4 0.2 - - - +
37D VAL* 3.8 0.5 - - - -
38D THR* 2.9 70.5 + - + +
40D VAL* 4.2 23.2 - - + +
54D VAL* 4.7 5.2 - - + -
55D SER* 1.3 79.9 - - - +
57D THR* 1.3 62.7 + - - +
59D THR* 3.3 28.3 - - + -
73D ALA* 3.5 18.6 - - + -
74D LYS 3.2 14.6 - - - +
75D LEU* 4.2 10.1 - - + -
76D CYS* 4.0 4.3 - - - -
82D VAL* 5.5 0.7 - - + -
84D ILE* 3.9 24.2 - - + +
116D PHE* 4.0 17.3 - + - -
131D VAL* 6.5 0.4 - - + -
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Residues in contact with THR 57 (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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36D LYS 3.1 26.2 + - - -
37D VAL* 4.1 13.5 - - + +
56D TYR* 1.3 76.2 - - - +
58D ASP* 1.3 91.9 + - - +
59D THR* 3.4 5.3 + - - -
73D ALA* 3.6 2.8 - - - +
74D LYS* 2.8 52.4 + - - +
76D CYS* 4.0 11.7 - - - -
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Residues in contact with ASP 58 (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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36D LYS 4.5 2.4 + - - +
57D THR* 1.3 93.9 + - - +
59D THR* 1.3 61.9 + - - +
60D LYS* 3.7 3.3 + - - +
72D GLN* 3.0 20.8 - - - +
73D ALA* 3.8 2.0 - - - -
74D LYS* 3.6 33.8 + - + +
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Residues in contact with THR 59 (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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290C GLU 5.2 0.7 - - - +
38D THR* 5.3 1.7 + - - -
56D TYR* 3.3 35.5 - - + -
57D THR* 4.2 3.0 - - - -
58D ASP* 1.3 75.2 - - - +
60D LYS* 1.3 63.7 + - - +
71D TYR* 3.5 37.9 - - + -
72D GLN 3.3 5.4 - - - +
73D ALA* 3.8 2.7 - - + +
84D ILE* 5.5 0.7 - - + -
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Residues in contact with LYS 60 (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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290C GLU 4.3 7.0 - - - +
291C PHE 4.6 1.1 - - - -
292C LYS* 3.0 46.6 - - + +
58D ASP 4.5 2.5 - - - +
59D THR* 1.3 78.4 - - - +
61D VAL* 1.3 66.3 + - - +
62D ILE* 3.4 14.1 + - + +
71D TYR* 3.3 5.3 - - - -
72D GLN* 2.8 60.9 + - + +
134D TYR* 5.7 3.1 + - - -
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Residues in contact with VAL 61 (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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263C VAL* 4.3 5.4 - - + +
288C TYR* 3.8 28.7 - - + -
289C THR 5.6 0.2 - - - +
290C GLU 3.7 15.4 + - - +
291C PHE* 3.4 46.2 - - + +
292C LYS* 4.7 1.9 + - - +
60D LYS* 1.3 74.3 - - - +
62D ILE* 1.3 65.5 + - - +
63D GLY 3.7 11.0 - - - +
69D VAL* 3.6 21.3 - - + -
70D VAL 3.7 4.0 - - - -
71D TYR* 3.6 26.0 - - + -
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Residues in contact with ILE 62 (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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261C SER* 5.2 4.3 + - - -
263C VAL* 3.5 20.0 - - - +
60D LYS* 3.6 15.3 - - + +
61D VAL* 1.3 78.8 - - - +
63D GLY* 1.3 58.8 + - - +
70D VAL* 2.7 38.3 + - + +
71D TYR 3.9 10.5 - - - +
72D GLN* 3.5 22.0 - - + -
83D ALA* 4.5 2.2 - - + -
134D TYR* 3.7 32.5 - - + +
502D I5R 4.1 21.1 - - + -
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Residues in contact with GLY 63 (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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261C SER* 6.3 1.6 - - - -
263C VAL* 3.4 8.7 - - - +
61D VAL* 3.7 3.8 - - - +
62D ILE* 1.3 82.0 - - - +
64D ASN* 1.3 62.9 + - - +
69D VAL* 3.4 13.3 - - - +
70D VAL* 3.0 28.8 + - - -
502D I5R 3.7 21.8 - - - -
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Residues in contact with ASN 64 (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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216C PTR 3.8 21.5 - - + +
223C ARG* 5.9 0.4 - - - +
227C LEU 4.6 1.8 + - - -
228C ILE* 3.1 42.4 + - - +
262C GLY* 4.1 24.8 + - - +
263C VAL* 4.0 8.9 - - + +
288C TYR* 2.2 32.6 + - - -
291C PHE* 5.6 0.2 - - - -
63D GLY* 1.3 76.6 - - - +
65D GLY* 1.3 62.0 + - - +
67D PHE* 3.9 9.4 - - - -
68D GLY 3.6 10.7 - - - +
502D I5R 4.3 6.9 - - - -
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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