Contacts of the strand formed by residues 55 - 66 (chain E) in PDB entry 3HB8
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 THR 55 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175D ARG* 4.9 5.6 + - - +
45E VAL 4.1 0.7 - - - -
46E ARG* 3.1 23.4 - - - +
47E LYS 2.9 18.5 + - - +
48E ASP 4.8 2.6 + - - -
49E ASP* 6.2 1.1 - - + +
54E GLY* 1.3 83.1 - - - +
56E LEU* 1.3 77.4 + - - +
57E SER* 3.7 14.0 + - - -
256E HIS* 3.6 32.7 - - + +
257E ILE 3.6 6.5 - - - -
258E TYR* 3.5 31.0 - - + +
259E LEU* 4.2 2.1 - - - +
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Residues in contact with LEU 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ILE* 2.9 50.4 - - + +
41E LEU* 3.5 37.5 - - + +
44E GLY* 3.8 11.9 - - - +
45E VAL 3.4 9.6 - - - -
46E ARG* 4.9 5.8 - - + +
55E THR* 1.3 96.2 - - - +
57E SER* 1.3 64.5 + - - +
58E VAL 3.7 0.3 + - - -
255E ALA 3.7 0.9 - - - +
256E HIS* 4.2 2.5 - - - -
257E ILE* 3.6 10.6 + - + +
259E LEU* 3.7 22.7 - - + -
262E ILE* 4.3 9.6 - - + -
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Residues in contact with SER 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ARG* 5.3 0.7 + - - -
202D TYR* 2.9 28.7 + - - -
45E VAL* 3.1 28.5 + - - +
47E LYS* 3.7 17.3 - - - +
55E THR* 3.7 7.0 + - - -
56E LEU* 1.3 74.9 - - - +
58E VAL* 1.3 58.6 + - - +
254E ASP* 2.7 30.0 + - - -
255E ALA 3.3 6.5 - - - -
256E HIS* 3.6 10.5 - - - +
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Residues in contact with VAL 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ARG* 4.7 5.4 - - - +
202D TYR* 4.4 0.4 - - - -
39E HIS* 4.2 23.3 - - + +
40E ILE* 3.6 29.2 - - + -
43E CYS 4.5 3.1 - - - +
44E GLY* 3.4 25.6 - - - +
56E LEU 3.9 0.4 - - - +
57E SER* 1.3 81.4 - - - +
59E PHE* 1.3 66.9 + - - +
60E GLY 3.6 3.1 + - - +
61E MET* 4.3 14.9 - - + +
253E GLY 3.6 0.2 - - - +
254E ASP* 4.6 2.0 - - - -
255E ALA* 2.8 32.2 + - - +
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Residues in contact with PHE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ARG* 2.8 33.4 + - - +
200D GLN* 3.1 52.9 - - + -
202D TYR* 3.2 57.3 - + + -
209D SER* 4.0 7.6 - - - +
210D CYS* 3.7 3.8 - - - -
211D GLN* 3.3 39.9 - - + -
249D ILE* 3.7 17.8 - - + +
58E VAL* 1.3 73.8 - - - +
60E GLY* 1.3 58.5 + - - +
253E GLY 3.1 25.1 - - - -
254E ASP* 4.0 1.6 - - - +
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Residues in contact with GLY 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLN* 3.7 7.9 - - - +
64D ARG* 2.7 25.0 + - - -
211D GLN* 4.2 4.3 - - - -
249D ILE* 4.0 19.5 - - - -
58E VAL* 3.6 1.8 + - - +
59E PHE* 1.3 72.0 - - - +
61E MET* 1.3 69.1 - - - +
252E LEU 3.5 7.4 - - - -
253E GLY 2.9 14.3 + - - -
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Residues in contact with MET 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLN* 3.2 11.9 + - - +
36E GLN* 3.4 49.8 - - + +
39E HIS* 3.4 35.0 - - + -
40E ILE* 3.6 23.3 - - + -
58E VAL* 4.3 8.7 - - + +
60E GLY* 1.3 83.1 - - - +
62E GLN* 1.3 63.4 + - - +
219E MET* 5.1 0.9 - - - -
250E HIS 4.1 0.2 - - - -
251E THR* 3.3 4.7 - - - -
252E LEU* 3.0 37.8 + - + -
255E ALA* 3.7 15.9 - - + -
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Residues in contact with GLN 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLY 3.5 4.2 - - - +
61D MET* 3.1 44.4 + - - +
62D GLN* 3.5 16.5 + - + +
251D THR* 3.7 4.2 - - - +
36E GLN* 3.8 5.3 + - - +
61E MET* 1.3 80.1 - - - +
63E ALA* 1.3 62.0 + - - +
211E GLN* 3.0 16.0 - - - +
249E ILE* 3.4 25.1 - - + +
250E HIS 2.9 4.3 - - - +
251E THR* 2.8 22.5 + - - +
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Residues in contact with ALA 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E GLN* 3.3 19.5 - - + +
36E GLN* 4.0 18.6 - - - +
62E GLN* 1.3 77.0 - - - +
64E ARG* 1.3 59.7 + - - +
65E TYR* 3.4 29.2 - - + +
248E PHE 3.5 2.3 - - - +
249E ILE* 3.4 3.1 - - - -
250E HIS* 2.7 44.2 + - + +
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Residues in contact with ARG 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D HIS* 5.4 5.5 + - - -
58D VAL* 4.4 11.1 - - - +
59D PHE 3.2 14.1 + - - -
60D GLY* 3.1 27.5 + - - -
29E GLY* 5.1 3.1 - - - +
32E GLN* 2.7 36.7 + - - +
63E ALA* 1.3 71.6 - - - +
65E TYR* 1.3 62.3 + - - +
66E SER 4.0 1.8 + - - +
247E ASP* 3.3 38.7 + - + +
248E PHE 3.8 2.2 - - - -
249E ILE* 3.4 28.5 - - + +
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Residues in contact with TYR 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E GLY* 3.5 31.4 - - - -
30E GLU* 5.0 1.8 - - - -
32E GLN* 4.4 4.5 - - - -
33E TYR* 3.5 23.7 - - + +
36E GLN* 4.0 3.6 + - - -
63E ALA* 3.4 30.3 - - + +
64E ARG* 1.3 74.2 - - - +
66E SER* 1.3 65.1 + - - +
67E LEU* 3.5 1.4 + - - +
72E PRO* 4.0 25.4 - - + -
74E LEU* 5.2 4.0 - - + -
227E ILE* 3.4 37.7 - - + +
247E ASP* 4.1 1.8 - - - -
248E PHE* 2.9 66.4 + + + +
250E HIS* 3.8 12.6 + - + -
276E PHE* 5.1 4.3 - + + -
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Residues in contact with SER 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E GLY* 6.0 2.2 - - - -
64E ARG* 4.0 4.0 + - - +
65E TYR* 1.3 74.1 - - - +
67E LEU* 1.3 64.6 + - - +
68E ARG* 3.3 30.5 + - - +
70E GLU* 3.6 33.0 + - - +
72E PRO* 4.4 6.1 - - - +
247E ASP* 3.4 17.2 + - - -
276E PHE* 5.8 1.0 - - - -
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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