Contacts of the strand formed by residues 35 - 43 (chain I) in PDB entry 3HEI
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 MET 35 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31I ILE* 3.4 5.3 - - - +
32I MET 3.0 31.1 + - - +
33I ASN* 2.9 39.5 - - + +
34I ASP* 1.3 80.2 - - - +
36I PRO* 1.4 74.4 - - + +
37I ILE* 3.5 6.4 + - + +
70L TYR* 4.6 2.7 - - - +
81L GLN* 2.5 46.7 - - + +
82L PRO* 3.4 35.0 - - + +
131L LYS* 3.7 25.6 - - + -
137L GLU* 5.6 0.4 - - - +
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Residues in contact with PRO 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ASN 3.8 5.2 - - - +
31I ILE* 4.0 10.3 - - + -
34I ASP 4.3 3.4 - - - +
35I MET* 1.4 85.3 - - + +
37I ILE* 1.3 64.4 + - - +
38I TYR* 5.1 4.8 - - + -
90J TRP* 3.5 31.4 - - + -
91J GLN* 6.2 0.2 - - - +
93J ASN* 6.1 2.7 - - - +
81L GLN* 5.9 0.2 + - - -
136L HIS* 6.1 2.9 - - - +
137L GLU* 6.1 2.7 - - + +
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Residues in contact with ILE 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I GLN* 3.4 4.7 - - - -
30I ASN 2.8 41.0 + - - +
32I MET* 3.9 28.7 - - + +
35I MET* 3.9 16.6 - - + +
36I PRO* 1.3 80.3 - - - +
38I TYR* 1.4 69.1 + - - +
39I MET* 3.7 19.5 - - + -
165I LEU* 3.6 30.7 - - + -
90J TRP* 3.9 3.5 - - - -
114J PHE* 4.3 2.0 - - + -
81L GLN* 5.2 8.5 - - - +
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Residues in contact with TYR 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I PHE* 3.6 19.7 - - + -
8I ALA* 6.0 0.5 - - - -
11I GLY* 3.1 27.5 + - - -
12I GLY* 3.4 29.4 - - - +
27I LEU* 4.1 24.2 - - + -
28I MET 3.3 8.3 - - - +
29I GLN* 3.5 33.0 + - + -
36I PRO* 5.1 3.8 - - + -
37I ILE* 1.4 87.4 - - - +
39I MET* 1.3 65.6 + - - +
165I LEU* 4.1 8.7 - - - +
90J TRP* 3.5 29.4 - + - -
102J GLU* 4.1 10.2 + - - -
103J LYS 5.0 0.9 + - - -
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Residues in contact with MET 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I PHE* 4.0 4.0 - - - -
27I LEU* 3.4 7.4 - - - -
28I MET* 2.8 46.1 + - + +
30I ASN* 3.2 28.5 - - + +
37I ILE* 3.7 23.6 - - + -
38I TYR* 1.3 77.6 - - - +
40I TYR* 1.3 63.7 + - - +
41I SER* 3.9 4.2 + - - -
163I ALA* 3.8 24.5 - - + -
164I LEU 3.4 15.7 - - - +
165I LEU* 3.7 13.0 - - + -
114J PHE* 3.6 37.5 - - + -
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Residues in contact with TYR 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I PHE* 3.6 34.8 - + - -
14I LEU 3.8 9.5 + - - -
15I GLY* 4.0 2.3 - - - -
16I TRP* 3.1 60.6 + + + -
18I THR* 4.7 8.1 - - + -
25I TRP* 3.9 9.7 - - + -
26I ASP 3.2 17.9 - - - -
27I LEU* 3.7 30.0 - - + +
39I MET* 1.3 72.9 - - - +
41I SER* 1.3 59.8 + - - +
54I LEU* 3.5 35.2 - - + -
163I ALA* 3.7 0.2 - - - -
164I LEU* 2.9 37.6 + - + +
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Residues in contact with SER 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I GLY 3.9 1.2 - - - +
25I TRP* 3.2 5.7 - - - -
26I ASP* 2.8 33.5 + - - +
28I MET* 3.4 31.4 - - - +
39I MET* 3.9 5.1 + - - -
40I TYR* 1.3 74.6 - - - +
42I VAL* 1.3 63.4 + - - +
162I VAL 3.2 13.5 - - - -
163I ALA* 4.0 7.6 - - - -
109J GLN* 4.8 3.7 + - - -
112J THR* 5.4 0.2 + - - -
113J PRO* 3.8 21.3 - - - +
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Residues in contact with VAL 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I GLY* 3.5 33.2 - - - +
25I TRP* 3.7 33.9 - - + +
41I SER* 1.3 78.6 + - - +
43I CYS* 1.4 65.0 + - - +
44I ASN* 4.4 9.2 - - - +
52I ASN* 3.9 4.5 - - + +
157I ASP* 3.6 38.1 - - + +
160I ALA 3.8 1.3 - - - +
161I CYS* 3.3 1.2 - - - -
162I VAL* 2.8 34.4 + - + +
109J GLN* 6.0 2.2 - - - +
113J PRO* 4.5 0.6 - - - +
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Residues in contact with CYS 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I VAL* 1.4 76.8 - - - +
44I ASN* 1.3 69.6 + - - +
45I VAL* 3.1 9.9 + - - +
81I PHE* 3.8 14.1 - - - -
160I ALA 3.4 8.7 - - - -
161I CYS* 2.1 47.6 - - - -
109J GLN* 5.4 3.9 - - - +
111J PHE* 3.9 37.6 - - - +
113J PRO* 4.3 5.2 - - + -
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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