Contacts of the strand formed by residues 52 - 64 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C VAL* 3.3 8.3 - - - +
42C ALA 2.9 33.3 + - - +
44C PRO* 3.9 24.7 - - - +
50C ARG* 4.4 3.3 + - + +
51C PRO* 1.3 76.7 - - - +
53C GLU* 1.3 68.3 - - - +
54C VAL* 3.5 11.4 + - + +
114C TYR* 4.1 20.7 + - + -
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Residues in contact with GLU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C THR* 4.6 17.5 - - + +
40C VAL 3.3 7.0 - - - +
41C VAL* 4.3 15.9 - - + -
52C GLN* 1.3 80.4 - - - +
54C VAL* 1.3 63.2 + - - +
55C SER* 5.2 0.4 - - - -
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Residues in contact with VAL 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C THR 3.9 0.5 - - - +
39C THR* 3.3 1.8 - - - -
40C VAL* 2.7 48.5 + - + +
42C ALA* 4.1 15.7 - - + -
52C GLN* 3.8 24.5 - - + +
53C GLU* 1.3 79.4 - - - +
55C SER* 1.3 67.0 + - - +
56C TYR* 4.7 4.1 - - + -
75C LEU* 4.2 17.9 - - + -
77C ASP* 5.0 5.4 - - - +
114C TYR* 4.2 36.3 - - + -
131C VAL* 6.4 0.9 - - + -
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Residues in contact with SER 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 4.1 6.9 - - - +
38C THR 3.3 6.5 - - - -
39C THR* 2.8 26.3 - - - +
53C GLU 5.2 0.9 - - - -
54C VAL* 1.3 76.2 - - - +
56C TYR* 1.3 63.2 + - - +
75C LEU* 3.5 7.6 - - - +
76C CYS* 2.9 41.2 + - - -
77C ASP* 3.8 8.5 + - - +
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Residues in contact with TYR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 3.8 0.9 - - - -
38C THR* 2.9 70.4 + - + +
40C VAL* 4.2 22.4 - - + +
54C VAL* 4.7 4.7 - - + -
55C SER* 1.3 79.0 - - - +
57C THR* 1.3 63.1 + - - +
59C THR* 3.3 28.5 - - + -
73C ALA* 3.5 18.2 - - + -
74C LYS 3.2 15.7 - - - +
75C LEU* 4.2 9.9 - - + -
76C CYS* 3.9 4.3 - - - -
82C VAL* 5.5 0.7 - - + -
84C ILE* 3.8 21.3 - - + +
116C PHE* 3.9 19.5 - + - -
131C VAL* 6.5 0.9 - - + -
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Residues in contact with THR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LYS 3.1 25.7 + - - -
37C VAL* 4.1 13.5 - - + +
56C TYR* 1.3 77.0 - - - +
58C ASP* 1.3 92.1 + - - +
59C THR* 3.4 5.6 - - - -
73C ALA* 3.6 2.6 - - - -
74C LYS* 2.9 52.2 + - - +
76C CYS* 4.2 10.8 - - - -
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Residues in contact with ASP 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LYS 4.5 2.2 + - - -
57C THR* 1.3 92.7 + - - +
59C THR* 1.3 62.8 + - - +
60C LYS* 3.7 3.2 + - - +
72C GLN* 3.0 19.1 - - - +
73C ALA* 3.8 2.4 - - - -
74C LYS* 3.6 35.0 + - + +
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Residues in contact with THR 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C THR* 5.3 1.7 + - - -
56C TYR* 3.3 35.8 - - + -
57C THR* 4.2 3.0 - - - -
58C ASP* 1.3 76.5 - - - +
60C LYS* 1.3 65.4 + - - +
71C TYR* 3.6 37.2 - - + -
72C GLN 3.3 6.3 - - - +
73C ALA* 3.9 2.8 - - + +
84C ILE* 5.5 0.2 - - + -
290D GLU 5.4 0.5 - - - +
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Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ASP 4.5 2.7 - - - +
59C THR* 1.3 77.7 - - - +
61C VAL* 1.3 66.3 + - - +
62C ILE* 3.4 14.7 + - + +
71C TYR* 3.3 4.6 - - - -
72C GLN* 2.8 63.1 + - + +
134C TYR* 5.6 2.7 - - - -
290D GLU 4.5 6.3 - - - +
291D PHE 4.9 0.9 - - - -
292D LYS* 3.4 44.8 - - + +
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LYS* 1.3 76.2 - - - +
62C ILE* 1.3 64.6 + - - +
63C GLY 3.7 12.1 - - - +
64C ASN* 5.6 0.2 - - - +
69C VAL* 3.7 21.8 - - + -
70C VAL 3.7 3.8 - - - -
71C TYR* 3.6 25.8 - - + -
263D VAL* 4.2 6.2 - - + +
288D TYR* 3.8 27.8 - - + -
290D GLU 3.8 14.5 + - - +
291D PHE* 3.5 42.2 - - + +
292D LYS* 5.0 1.4 + - - +
293D PHE* 5.4 2.4 - - - -
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LYS* 3.6 15.3 - - + +
61C VAL* 1.3 78.2 - - - +
63C GLY* 1.3 57.5 + - - +
70C VAL* 2.7 37.7 + - + +
71C TYR 3.9 9.9 - - - +
72C GLN* 3.6 22.2 - - + -
83C ALA* 4.5 3.6 - - + -
134C TYR* 3.7 33.2 - - + +
502C I5R 3.9 21.8 - - + -
261D SER* 5.0 4.9 + - - -
263D VAL* 3.7 19.1 - - - +
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Residues in contact with GLY 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 3.7 4.0 - - - +
62C ILE* 1.3 81.1 - - - +
64C ASN* 1.3 63.2 + - - +
69C VAL* 3.4 13.0 - - - +
70C VAL* 3.0 29.8 + - - -
502C I5R 3.6 20.2 - - - -
261D SER* 6.1 1.1 - - - -
263D VAL* 3.5 8.9 - - - +
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Residues in contact with ASN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 5.6 0.2 - - - +
63C GLY* 1.3 76.7 - - - +
65C GLY* 1.3 61.3 + - - +
67C PHE* 4.0 9.9 - - - -
68C GLY 3.5 10.4 - - - +
69C VAL* 4.7 0.4 - - - +
502C I5R 4.2 8.2 - - - -
216D PTR 3.7 19.7 - - + +
227D LEU 4.8 1.8 + - - -
228D ILE* 3.2 40.8 + - - +
261D SER* 6.2 0.2 - - - -
262D GLY* 4.1 24.9 + - - +
263D VAL* 4.0 9.7 - - + +
288D TYR* 2.8 30.7 + - - -
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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