Contacts of the strand formed by residues 30 - 36 (chain D) in PDB entry 2ESV
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 TYR 30 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLU* 3.1 42.7 - - + +
155A HIS* 3.8 29.3 + + - +
158A ALA* 3.5 18.1 - - + +
29D ASN 3.5 19.1 - - - +
30D GLU* 1.3 73.7 - - - +
31D VAL* 1.3 62.4 + - - +
32D TYR* 3.5 30.2 + - - -
47D HIS* 4.5 13.7 - + - -
48D GLY 3.9 9.9 + - - +
49D LEU* 3.5 36.7 - - + +
91D VAL* 3.3 5.4 - - - -
92D VAL 2.8 38.6 + - - -
94D SER* 3.9 4.7 - - - +
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Residues in contact with VAL 31 (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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23D HIS* 3.5 26.5 - - + +
26D ILE* 3.7 22.7 - - + -
30D TYR* 1.3 70.1 + - - -
32D TYR* 1.3 62.1 + - - +
33D TRP* 3.9 21.1 - - + +
47D HIS* 3.2 4.0 - - - +
48D GLY 2.9 41.1 + - - +
49D LEU* 5.1 0.2 - - - +
63D LEU* 4.1 4.7 - - + +
65D ILE* 4.5 12.6 - - + -
69D ARG* 4.8 4.0 - - - +
72D SER* 3.4 21.5 - - - +
89D CYS* 4.2 11.7 - - - -
90D ILE 4.0 2.7 - - - +
91D VAL* 4.0 3.4 - - + -
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Residues in contact with TYR 32 (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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155A HIS* 4.5 4.9 - - - -
30D TYR* 3.5 30.4 + - - -
31D VAL* 1.3 74.9 - - - +
33D TRP* 1.3 67.3 + - - +
34D TYR* 4.2 19.3 - + + -
44D TYR* 4.4 5.8 - + - -
46D ILE 3.7 2.5 - - - -
47D HIS* 3.2 35.6 - + + -
89D CYS* 3.5 4.0 - - - -
90D ILE* 2.8 40.4 + - + +
92D VAL* 3.4 40.1 + - + +
103D LEU* 4.9 2.9 - - + -
98E ARG 5.1 0.8 + - - -
99E ASP* 2.9 55.0 + - - -
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Residues in contact with TRP 33 (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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7D GLN* 3.5 19.3 - - - -
19D LEU* 3.6 29.6 - - + -
20D PRO 3.8 6.5 - - - -
21D CYS* 3.4 27.1 - - + -
31D VAL* 3.9 13.5 - - + +
32D TYR* 1.3 78.9 - - - +
34D TYR* 1.3 65.8 + - - +
44D TYR* 4.7 0.2 - - - -
45D ILE* 3.0 26.0 + - + +
46D ILE* 2.9 22.7 + - + +
63D LEU* 3.3 32.5 - - + +
72D SER* 4.3 3.5 - - - -
74D LEU* 3.7 52.7 - - + -
87D TYR* 4.4 7.6 - - + -
88D TYR 3.3 16.4 - - - -
89D CYS* 3.6 14.4 - - + -
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Residues in contact with TYR 34 (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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32D TYR* 4.2 15.0 - + + -
33D TRP* 1.3 80.8 - - - +
35D ARG* 1.3 62.4 + - - +
42D PRO* 4.6 2.2 - - + -
43D GLN 3.3 11.2 - - - +
44D TYR* 3.4 36.4 - + - -
45D ILE* 3.7 5.2 - - - +
87D TYR* 3.7 2.1 - - - +
88D TYR* 2.8 32.4 + - + +
90D ILE* 4.3 11.9 - - + -
103D LEU* 3.6 33.3 - - + +
105D PHE* 4.4 16.8 - + + -
99E ASP 3.7 10.9 + - - -
106E GLN* 3.0 48.3 + - - +
108E PHE* 3.8 19.3 - + - -
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Residues in contact with ARG 35 (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 TYR* 1.3 75.0 - - - +
36D GLN* 1.3 61.9 + - - +
37D ILE* 4.0 23.4 + - + +
41D GLY 4.4 0.2 - - - +
42D PRO* 3.3 2.8 - - - +
43D GLN* 2.6 72.6 + - + +
45D ILE* 3.5 13.9 - - + +
58D MET* 3.6 24.0 - - - +
76D LEU* 4.8 3.0 - - - +
82D ARG* 4.6 4.0 + - - +
83D ASP* 2.6 32.5 + - - +
85D ALA* 4.1 9.0 - - + -
86D VAL 3.2 13.0 - - - +
87D TYR* 3.0 38.1 + - + -
88D TYR* 4.5 3.6 - - - -
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Residues in contact with GLN 36 (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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35D ARG* 1.3 75.0 - - - +
37D ILE* 1.3 59.3 + - - +
38D HIS 3.2 19.5 + - - +
39D SER 3.7 3.4 - - - -
40D GLN 3.1 24.9 + - - +
41D GLY 4.9 0.7 - - - -
42D PRO* 4.3 10.4 - - + +
85D ALA* 3.2 4.1 - - - +
86D VAL* 2.9 39.9 + - + +
88D TYR* 3.6 21.0 + - + +
1001D IOD 3.3 26.0 - - - +
37E ARG* 3.0 25.9 + - - +
43E ILE* 3.8 7.6 - - - +
91E PHE* 3.7 12.5 - - - -
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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