Contacts of the strand formed by residues 24 - 32 (chain D) in PDB entry 1EVW
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 VAL 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C VAL* 6.0 1.1 - - + -
20D GLY 5.3 1.1 - - - +
22D PHE 3.9 3.6 - - - +
23D PRO* 1.3 71.7 - - - +
25D ILE* 1.3 71.8 + - - +
26D THR* 4.3 3.6 + - - +
40D HIS* 3.7 33.2 - - + -
41D CYS 3.4 6.1 - - - +
42D TYR* 3.4 39.3 - - + +
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Residues in contact with ILE 25 (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 PRO* 4.2 17.7 - - + +
24D VAL* 1.3 82.1 - - - +
26D THR* 1.3 64.7 + - - +
27D HIS* 3.4 32.6 + - + +
39D LEU 3.3 1.9 - - - +
40D HIS* 3.1 6.4 - - - -
41D CYS 2.8 37.4 + - - +
43D GLU* 3.3 38.1 - - + +
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Residues in contact with THR 26 (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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24D VAL* 5.1 3.1 + - - +
25D ILE* 1.3 76.5 - - - +
27D HIS* 1.3 66.7 + - - +
28D HIS* 4.4 5.8 + - + -
38D THR* 3.5 27.6 - - + -
39D LEU 3.3 2.0 - - - -
40D HIS* 3.6 23.2 - - + +
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Residues in contact with HIS 27 (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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25D ILE* 3.4 29.2 - - + +
26D THR* 1.3 76.4 + - - +
28D HIS* 1.3 64.1 + - - +
29D VAL* 3.7 13.5 + - + -
38D THR* 3.3 4.9 - - - -
39D LEU* 2.7 47.2 + - + +
41D CYS* 4.6 10.5 - - + -
43D GLU* 3.4 23.1 + - - -
102D ASN* 4.0 12.3 + - + -
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Residues in contact with HIS 28 (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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26D THR* 5.6 4.1 + - + -
27D HIS* 1.3 72.5 + - - +
29D VAL* 1.3 65.5 + - - +
30D PRO* 4.5 1.2 - - - +
36D GLN* 3.4 30.8 + - + +
37D GLY 3.3 16.6 - - - +
38D THR* 3.7 20.9 + - + +
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Residues in contact with VAL 29 (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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27D HIS* 4.3 17.9 - - + +
28D HIS* 1.3 81.5 - - - +
30D PRO* 1.3 69.1 - - + +
31D LEU* 3.5 5.6 + - + +
36D GLN* 3.7 5.0 - - - +
37D GLY 2.9 31.6 + - - +
39D LEU* 4.0 25.8 - - + -
100D CYS 5.6 0.7 - - - +
139D LEU 4.3 4.5 - - - +
140D ARG* 3.5 50.7 - - + +
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Residues in contact with PRO 30 (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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28D HIS 4.5 1.8 - - - +
29D VAL* 1.3 87.8 - - + +
31D LEU* 1.3 59.3 + - - +
32D GLY* 3.3 1.3 - - - +
35D LEU 3.6 8.5 - - - +
36D GLN* 4.0 12.1 - - + +
140D ARG* 3.7 23.3 - - - +
141D GLN* 2.8 52.3 + - - +
142D GLY 5.5 0.4 - - - +
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Residues in contact with LEU 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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29D VAL* 3.8 6.5 - - + +
30D PRO* 1.3 73.9 - - - +
32D GLY* 1.3 59.3 + - - +
35D LEU* 2.9 22.0 + - + +
36D GLN 3.0 32.8 - - - +
37D GLY* 3.5 20.2 - - - +
38D THR 5.1 0.2 - - - +
39D LEU* 5.7 3.6 - - + -
127D GLY* 3.1 6.1 - - - -
128D PRO* 3.0 28.1 - - + +
129D ASN* 2.8 42.3 + - + +
139D LEU 4.0 18.4 - - - +
140D ARG* 4.6 0.7 - - - +
141D GLN* 4.2 0.4 - - - +
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Residues in contact with GLY 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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30D PRO* 3.3 4.2 - - - +
31D LEU* 1.3 81.2 - - - +
33D GLY* 1.3 62.5 + - - -
34D GLY 3.0 7.6 - - - -
35D LEU* 3.0 14.5 + - - +
126D PRO 3.6 12.6 - - - -
129D ASN* 3.0 18.9 - - - +
130D GLY* 3.5 7.9 - - - -
141D GLN* 3.8 11.6 - - - +
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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