Contacts of the strand formed by residues 39 - 48 (chain E) in PDB entry 2Z7F
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 GLY 39 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E GLN* 3.2 4.8 - - - +
35E LEU* 2.9 34.2 + - - +
36E ARG 3.2 2.5 + - - -
38E GLY* 1.3 78.6 - - - +
40E HIS* 1.3 67.5 + - - -
41E PHE* 3.4 2.4 + - - +
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Residues in contact with HIS 40 (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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30E MET* 5.6 0.2 - - + -
32E SER* 2.8 22.3 + - - +
33E LEU 3.5 6.1 - - - -
34E GLN* 3.9 9.0 - - - +
39E GLY* 1.3 73.0 - - - -
41E PHE* 1.3 62.0 + - - +
42E CYS 3.2 30.1 + - - -
43E GLY* 3.8 4.3 - - - -
73E LEU* 3.5 25.6 - - + +
141E TRP* 3.9 37.9 - + + +
151E ILE* 4.8 10.6 - - + +
193E GLY* 2.9 30.6 + - - -
74I LEU* 4.2 12.6 - - + +
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Residues in contact with PHE 41 (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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33E LEU* 2.9 52.5 + - + -
34E GLN 3.6 4.3 - - - -
35E LEU* 3.6 45.3 - - + -
39E GLY 4.4 1.8 - - - +
40E HIS* 1.3 81.1 - - - +
42E CYS* 1.3 83.9 + - + +
58E CYS* 3.3 27.1 - - + -
59E VAL* 4.5 1.8 - - + -
62E VAL* 4.4 3.6 - - + -
65E VAL* 4.0 22.0 - - + -
193E GLY* 4.6 10.0 - - - -
73I MET* 3.9 24.6 - - + +
74I LEU* 5.0 6.6 + - - +
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Residues in contact with CYS 42 (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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33E LEU* 2.8 35.8 + - + +
40E HIS* 3.2 15.7 + - - -
41E PHE* 1.3 100.9 - - + +
43E GLY* 1.3 60.5 + - - +
58E CYS* 2.1 56.8 - - + -
193E GLY 4.3 1.8 - - - -
195E SER* 3.5 15.5 - - - +
73I MET* 4.1 6.3 - - - -
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Residues in contact with GLY 43 (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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30E MET* 4.1 4.9 - - - -
31E VAL 3.3 10.3 - - - -
33E LEU* 4.0 0.7 - - - +
40E HIS* 3.8 6.8 + - - -
42E CYS* 1.3 76.9 - - - +
44E ALA* 1.3 57.3 + - - +
54E SER* 2.8 27.2 + - - -
193E GLY 4.3 0.6 + - - -
195E SER 2.8 10.3 + - - -
196E GLY* 3.2 10.6 - - - +
197E SER* 3.6 19.3 + - - -
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Residues in contact with ALA 44 (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 PHE 3.9 0.7 - - - +
30E MET* 4.0 0.2 - - - +
31E VAL* 3.0 48.0 + - + -
33E LEU* 4.0 12.8 - - + -
43E GLY* 1.3 76.3 - - - +
45E THR* 1.3 65.8 + - - +
52E VAL* 4.3 8.3 - - + -
53E MET 3.3 15.7 - - - +
54E SER* 3.9 8.7 - - - -
196E GLY 3.4 6.8 + - - -
197E SER* 4.4 0.8 - - - +
198E PRO* 3.9 9.1 - - - +
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Residues in contact with THR 45 (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 PHE* 3.4 15.9 - - + -
31E VAL* 4.0 3.1 - - - -
44E ALA* 1.3 74.7 - - - +
46E LEU* 1.3 65.2 + - - +
47E ILE* 3.4 8.9 + - + +
52E VAL* 3.2 4.1 - - - -
53E MET* 2.9 47.9 + - + +
121E ALA* 3.5 31.2 - - + -
196E GLY 4.7 1.2 + - - -
198E PRO* 3.2 28.1 - - - +
209E ILE* 4.1 11.0 - - + +
212E ILE* 5.7 1.6 - - - +
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Residues in contact with LEU 46 (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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28E PRO 4.9 1.1 - - - +
29E PHE* 2.9 19.4 + - - +
31E VAL* 3.6 7.4 - - + +
45E THR* 1.3 69.4 - - - +
47E ILE* 1.3 59.5 + - - +
48E ALA 3.1 26.0 - - - +
49E PRO 4.2 7.4 - - - +
51E PHE 3.6 8.7 - - - +
52E VAL* 3.8 14.4 - - + -
68E LEU* 4.1 19.1 - - + -
108E LEU* 4.4 2.9 - - + -
112E ALA* 4.5 5.4 - - + -
114E ILE* 4.6 2.2 - - + -
118E VAL* 3.6 31.4 - - + -
119E GLN 3.6 22.9 - - - +
120E VAL* 3.6 6.0 - - + +
121E ALA* 2.8 30.8 + - - +
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Residues in contact with ILE 47 (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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45E THR* 3.4 9.2 + - + +
46E LEU* 1.3 78.4 - - - +
48E ALA* 1.3 60.3 + - - +
51E PHE* 3.0 28.1 + - + +
52E VAL 4.3 3.1 - - - -
53E MET* 3.7 50.0 - - + +
105E ILE* 4.4 8.3 - - + -
120E VAL* 3.2 19.8 - - - +
121E ALA* 4.5 4.5 - - + +
123E LEU* 4.3 16.8 - - + +
238E ILE* 3.7 27.8 - - + -
242E ILE* 3.7 28.9 - - + +
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Residues in contact with ALA 48 (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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46E LEU* 3.1 19.8 - - - +
47E ILE* 1.3 77.1 - - - +
49E PRO* 1.4 76.7 - - + +
50E ASN* 3.0 4.7 + - - +
51E PHE* 3.2 34.2 + - + +
120E VAL* 3.7 11.9 - - - +
242E ILE* 4.6 13.9 - - + +
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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