Contacts of the strand formed by residues 56 - 69 (chain D) in PDB entry 5CLQ
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 GLU 56 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207C THR* 4.6 4.0 - - - -
50D PHE* 3.6 9.8 - - - -
51D ASP* 2.7 38.6 + - + +
54D SER* 3.2 30.5 + - - +
55D LYS* 1.3 82.5 - - - +
57D TRP* 1.3 64.5 + - - +
58D LYS* 4.6 7.8 - - + +
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Residues in contact with TRP 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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204C ALA* 3.7 29.4 + - + -
207C THR* 2.6 37.3 + - + +
208C ALA 3.4 8.9 + - - +
209C LEU* 3.3 19.0 - - + +
210C PRO* 3.9 29.8 - - + +
48D PHE* 3.9 14.6 - - + -
49D ARG 3.5 8.1 - - - -
50D PHE* 3.4 28.0 - + + -
56D GLU* 1.3 77.1 - - - +
58D LYS* 1.3 62.3 - - - +
103D ASN* 3.8 0.8 - - - +
111D VAL* 3.7 21.1 - - + -
126D GLN* 3.3 23.6 - - + -
127D LEU 3.6 17.0 - - - -
128D ALA* 3.3 21.5 - - + -
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Residues in contact with LYS 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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34C GLU* 3.6 34.9 + - + +
210C PRO* 5.9 0.2 - - - -
48D PHE* 3.4 5.2 - - - -
49D ARG* 2.6 77.6 + - + +
51D ASP* 3.4 42.3 + - + +
54D SER* 4.9 2.5 - - - +
56D GLU* 3.7 10.3 + - - +
57D TRP* 1.3 78.7 - - - +
59D GLU* 1.3 62.6 + - - +
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Residues in contact with GLU 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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29C ARG* 3.4 28.9 + - - +
32C THR 4.1 1.0 - - - +
33C GLY 3.9 5.2 - - - +
34C GLU* 3.1 28.9 + - - +
35C PHE 5.1 2.0 - - - +
154C ASN* 5.4 2.8 + - - -
210C PRO* 5.7 2.0 - - + +
46D LYS* 3.8 32.9 + - + +
47D LEU 3.8 6.1 - - - +
48D PHE* 3.9 19.0 - - + -
49D ARG* 5.5 0.6 - - - +
58D LYS* 1.3 74.5 - - - +
60D ARG* 1.3 61.1 + - - +
61D GLY* 3.8 17.7 + - - +
62D ILE* 4.7 8.0 + - - +
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Residues in contact with ARG 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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32C THR* 3.2 26.4 + - - +
33C GLY* 3.4 4.7 - - - -
47D LEU* 2.9 23.6 + - + +
48D PHE 4.5 0.2 - - - -
49D ARG* 2.8 62.8 - - + +
58D LYS 3.6 0.8 + - - -
59D GLU* 1.3 74.0 - - - +
61D GLY* 1.3 59.7 + - - +
82D ARG* 3.1 33.7 + - - +
89D CYS* 3.1 35.5 + - + +
116D ASP* 4.9 1.4 + - - -
118D ALA* 4.3 8.3 - - - +
119D ASP* 2.1 43.0 + - - -
123D LYS* 5.5 0.2 - - - +
125D GLU* 4.5 9.5 + - - -
127D LEU* 5.0 4.5 - - - -
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Residues in contact with GLY 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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33C GLY* 5.3 0.7 - - - -
46D LYS* 3.5 2.1 - - - +
47D LEU* 2.5 40.9 + - - +
59D GLU* 3.8 11.9 - - - +
60D ARG* 1.3 80.9 - - - +
62D ILE* 1.3 58.0 + - - -
80D MET* 3.9 5.3 - - - +
82D ARG* 4.2 13.9 - - - -
89D CYS* 4.4 8.7 - - - -
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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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154C ASN* 4.2 17.9 - - - +
44D ARG* 3.3 37.7 - - - +
45D ALA 3.3 15.5 - - - +
46D LYS* 4.5 25.4 - - + +
59D GLU* 4.8 7.2 - - - +
61D GLY* 1.3 75.0 - - - +
63D GLY* 1.3 62.5 + - - +
80D MET* 3.9 1.6 - - - -
81D ARG 4.1 1.8 - - - -
82D ARG* 3.6 5.6 - - + +
83D GLU* 2.9 45.4 + - + +
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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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44D ARG* 4.0 5.8 - - - -
45D ALA 2.8 31.4 + - - +
62D ILE* 1.3 76.8 - - - +
64D ASN* 1.3 65.1 + - - -
80D MET* 3.3 11.1 - - - +
81D ARG 3.3 11.2 - - - -
83D GLU* 4.3 11.7 - - - -
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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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42D CYS* 4.3 18.9 - - - -
43D ASN* 3.5 5.1 - - - +
44D ARG* 3.3 27.9 + - - +
63D GLY* 1.3 70.5 - - - -
65D VAL* 1.3 61.7 + - - +
66D LYS* 3.9 3.9 + - - +
79D LEU 3.7 1.4 - - - +
80D MET* 3.6 18.3 - - - -
81D ARG 3.7 9.3 + - - -
202D SO4 3.5 39.0 + - - +
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Residues in contact with VAL 65 (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 PHE* 3.5 10.5 - - + +
42D CYS* 3.2 6.9 + - - +
43D ASN 2.8 31.3 + - - +
45D ALA* 3.5 32.5 - - + -
64D ASN* 1.3 72.3 - - - +
66D LYS* 1.3 64.3 + - - +
78D LEU* 4.0 33.2 - - + -
79D LEU 3.5 3.8 - - - +
80D MET* 3.7 17.5 - - + -
129D ILE* 3.5 23.3 - - + -
131D PHE* 4.6 2.0 - - + -
140D PHE* 4.2 7.6 - - + -
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Residues in contact with LYS 66 (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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34D GLU* 3.3 27.4 + - - +
39D GLU* 4.1 14.4 - - + +
41D PHE 3.1 7.6 - - - +
42D CYS* 3.9 20.6 - - + -
64D ASN 4.2 5.8 + - - +
65D VAL* 1.3 81.1 - - - +
67D ILE* 1.3 63.5 + - - +
68D LEU* 3.9 19.9 + - + -
77D ARG 3.8 0.3 - - - +
78D LEU* 3.4 6.1 - - - +
79D LEU* 2.7 48.4 + - + +
81D ARG* 4.2 7.7 - - - +
202D SO4 2.5 46.9 + - - -
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Residues in contact with ILE 67 (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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40D PHE* 2.6 45.2 + - + +
41D PHE* 3.1 33.2 + - + -
66D LYS* 1.3 75.2 - - - +
68D LEU* 1.3 65.2 + - - +
76D ILE* 3.6 23.6 - - + -
77D ARG 3.5 2.5 - - - -
78D LEU* 4.6 4.7 - - + -
94D ILE* 4.0 15.9 - - + -
140D PHE* 4.1 23.6 - - + -
143D LYS* 3.9 6.3 - - + +
144D PHE* 3.7 31.2 - - + +
147D ALA* 4.3 7.4 - - + -
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Residues in contact with LEU 68 (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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34D GLU* 4.1 20.9 - - + +
37D GLU* 2.8 24.5 - - + +
38D GLU 3.3 17.7 - - - +
39D GLU* 3.8 12.6 - - + -
40D PHE* 5.3 0.7 - - - -
66D LYS* 3.9 21.3 - - + +
67D ILE* 1.3 83.7 - - - +
69D ARG* 1.4 51.1 + - - +
70D HIS 4.3 0.2 - - - -
75D LYS 3.6 1.0 - - - +
76D ILE* 2.9 13.9 - - - +
77D ARG* 2.7 62.0 + - + +
79D LEU* 4.1 31.2 - - + -
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Residues in contact with ARG 69 (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 GLU* 2.5 30.3 + - - +
38D GLU* 3.0 29.2 + - - -
40D PHE* 3.5 26.3 - - + -
68D LEU* 1.4 69.4 - - - +
70D HIS* 1.3 66.4 + - - +
71D LYS* 3.3 54.0 + - - +
74D GLY* 4.6 8.4 - - - +
75D LYS 3.2 5.8 - - - +
76D ILE* 3.8 20.2 - - + -
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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