Contacts of the strand formed by residues 35 - 41 (chain A) in PDB entry 1SFE
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 ILE 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.2 9.2 - - + -
29A ALA 3.4 14.6 - - - +
30A GLU* 4.0 26.7 - - + +
34A GLY* 1.3 67.5 - - - -
36A CYS* 1.3 55.8 + - - +
37A ALA 4.1 2.0 - - - +
38A ILE* 3.7 35.9 - - + -
67A PHE* 5.6 0.4 - - + -
70A HIS* 4.8 3.4 - - + +
74A VAL* 3.8 28.3 - - + -
85A LEU* 4.4 8.7 - - + -
87A LEU* 4.4 12.8 - - + -
88A PRO 3.0 12.3 + - - +
89A LEU* 3.6 10.3 - - + +
90A ASP 2.7 27.0 + - - +
140A LEU* 3.9 10.9 - - + +
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Residues in contact with CYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.0 10.8 - - - -
29A ALA* 3.0 32.0 + - - -
30A GLU 3.8 3.6 - - - -
31A SER* 3.9 13.5 - - - +
34A GLY 3.1 3.0 + - - +
35A ILE* 1.3 71.6 - - - +
37A ALA* 1.3 63.5 + - - +
55A PHE* 3.7 33.8 - - + -
90A ASP* 3.6 35.5 - - + +
92A ARG* 5.4 0.6 - - - +
139A LYS* 4.2 10.9 - - - +
140A LEU* 3.7 7.2 - - - +
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Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.2 1.1 - - + -
28A VAL* 3.5 1.2 - - - -
29A ALA* 2.9 35.6 + - + +
35A ILE* 4.1 0.2 - - - +
36A CYS* 1.3 81.3 - - - +
38A ILE* 1.3 67.9 + - - +
39A LEU* 4.1 11.0 - - + -
51A LEU* 3.8 27.8 - - + -
54A MET* 5.1 1.6 - - + -
55A PHE* 4.1 6.5 - - + -
139A LYS* 3.2 15.5 - - + +
140A LEU* 3.4 4.0 - - - +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 5.1 1.1 - - + -
27A LEU 3.3 6.5 - - - +
28A VAL* 4.5 5.2 - - + -
35A ILE* 3.7 20.9 - - + -
37A ALA* 1.3 79.8 - - - +
39A LEU* 1.3 65.7 + - - +
40A LEU* 4.9 3.1 - - + -
74A VAL* 3.8 22.2 - - + -
78A LEU* 3.9 26.5 - - + -
85A LEU* 4.6 2.0 - - + -
139A LYS 2.9 11.2 + - - +
140A LEU* 3.9 7.5 - - + +
141A ALA* 3.1 44.6 + - + +
143A VAL* 3.5 33.7 - - + -
161A TRP* 3.8 1.4 - - - -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 3.1 7.4 - - - +
27A LEU* 2.8 45.1 + - + +
37A ALA* 4.4 3.8 - - + -
38A ILE* 1.3 85.4 - - - +
40A LEU* 1.3 62.2 + - - +
47A LEU* 4.1 18.8 - - + +
50A GLU* 4.0 15.5 - - + +
51A LEU* 3.9 28.7 - - + +
54A MET* 3.5 36.8 - - + -
139A LYS 3.9 12.1 - - - +
160A ARG* 4.4 3.6 - - - +
161A TRP* 4.0 16.4 - - + +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A CYS* 4.3 15.5 - - - -
23A LEU* 4.3 15.0 - - + +
25A ARG 3.4 3.8 - - - +
26A CYS* 3.7 22.9 - - + -
38A ILE* 4.9 5.6 - - + -
39A LEU* 1.3 76.0 - - - +
41A GLY* 1.3 60.6 + - - +
47A LEU* 3.4 10.5 - - - +
50A GLU* 4.9 1.6 - - - +
78A LEU* 5.0 2.5 - - + -
141A ALA* 3.8 26.5 - - + -
142A ILE* 4.5 15.0 - - + -
159A TYR* 4.2 13.9 - - - +
161A TRP* 3.2 31.8 - - + +
165A ARG* 3.7 32.3 + - + -
169A LEU* 5.1 0.4 - - + -
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLY* 4.0 1.0 - - - -
25A ARG* 2.8 40.0 + - - +
40A LEU* 1.3 76.8 - - - +
42A ASP* 1.3 62.7 + - - +
43A ASP 3.7 0.7 - - - -
46A THR* 5.7 0.9 - - - -
47A LEU* 3.9 12.3 - - - +
165A ARG* 3.4 22.6 + - - +
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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