Contacts of the helix formed by residues 35 - 45 (chain D) in PDB entry 5CYP
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 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D GLY 3.3 2.4 + - - -
34D LEU* 1.3 80.4 - - - +
36D LYS* 1.3 64.1 + - - +
37D SER 3.5 2.2 - - - -
38D THR* 3.5 2.2 + - - -
39D LEU* 3.1 23.7 + - - +
139D PHE* 4.0 4.0 - - - -
226D GLY* 5.6 0.7 - - - -
301D GSP 2.9 45.6 + - - -
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Residues in contact with LYS 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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28D VAL* 4.3 8.2 - - + +
29D VAL* 3.7 10.5 - - - +
30D GLY* 2.5 55.7 + - - +
31D GLN 3.6 0.9 + - - +
34D LEU* 4.5 4.3 - - + -
35D GLY* 1.3 74.6 - - - +
37D SER* 1.3 65.6 + - - +
39D LEU* 3.2 11.8 + - - +
40D ILE* 3.3 18.5 + - - +
87D ASP* 4.3 8.1 - - - +
88D THR* 3.5 18.4 + - - -
89D PRO 3.8 1.6 + - - -
90D GLY* 3.0 25.5 - - - +
139D PHE* 3.6 33.7 - - + -
301D GSP 3.2 28.0 + - - +
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Residues in contact with SER 37 (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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36D LYS* 1.3 76.8 - - - +
38D THR* 1.3 63.5 + - - +
40D ILE* 3.2 22.7 + - - +
41D ASN* 3.6 8.3 + - - +
61D ILE* 3.7 30.6 - - - +
64D THR* 3.1 3.8 + - - -
87D ASP* 2.9 15.0 + - - -
301D GSP 2.6 10.5 + - - -
302D MG 2.0 35.2 - - - -
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Residues in contact with THR 38 (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 GLY 3.8 3.1 - - - -
36D LYS 3.2 0.4 - - - -
37D SER* 1.3 76.9 - - - +
39D LEU* 1.3 52.1 + - - +
41D ASN* 2.6 12.6 - - - +
42D THR* 2.5 30.8 + - - +
61D ILE* 3.8 19.4 - - + +
226D GLY* 3.9 17.7 - - - +
301D GSP 2.5 65.3 + - + +
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Residues in contact with LEU 39 (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 VAL* 5.1 3.1 - - + -
35D GLY 3.1 16.9 + - - +
36D LYS 3.6 5.8 - - - +
37D SER 3.2 0.4 - - - -
38D THR* 1.3 77.2 - - - +
40D ILE* 1.3 53.5 + - + +
41D ASN 3.6 0.2 - - - -
42D THR* 3.3 4.8 - - - -
43D LEU* 2.8 34.9 + - + +
137D LEU* 4.1 18.2 - - + -
139D PHE* 3.5 25.8 - - + -
167D VAL* 5.8 0.4 - - + -
224D VAL* 4.0 24.2 - - + -
225D VAL 4.4 16.8 - - - +
226D GLY* 4.6 3.6 - - - +
258D PHE* 3.5 40.7 - - + -
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Residues in contact with ILE 40 (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 VAL* 3.7 18.2 - - + -
36D LYS 3.3 13.0 - - - +
37D SER* 3.2 8.9 + - - +
39D LEU* 1.3 73.6 - - - +
41D ASN* 1.3 62.1 + - - +
43D LEU* 3.0 10.0 + - - +
44D PHE* 3.0 40.0 + - + -
70D ILE* 4.2 18.2 - - + -
85D VAL* 3.6 35.9 - - + -
87D ASP* 3.5 42.4 - - + +
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Residues in contact with ASN 41 (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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37D SER 3.6 5.9 + - - +
38D THR* 2.6 33.2 - - - +
40D ILE* 1.3 79.6 - - - +
42D THR* 1.3 64.8 + - - +
44D PHE* 4.0 8.5 - - - +
45D LYS* 2.9 32.4 + - - +
61D ILE* 4.3 17.2 - - - +
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Residues in contact with THR 42 (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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38D THR* 2.5 25.7 + - - +
39D LEU* 3.3 14.1 - - + -
40D ILE 3.1 0.2 - - - -
41D ASN* 1.3 86.8 + - - +
43D LEU* 1.3 62.7 + - - +
45D LYS* 3.4 19.7 + - - +
225D VAL 4.9 10.5 - - - +
226D GLY 4.4 9.7 - - - -
258D PHE* 3.9 24.1 - - + -
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Residues in contact with LEU 43 (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 ILE* 4.2 23.3 - - + -
39D LEU* 2.8 18.7 + - + +
40D ILE* 3.0 9.6 + - - +
42D THR* 1.3 75.7 - - - +
44D PHE* 1.3 61.5 + - + +
45D LYS 3.7 4.3 - - - +
83D LEU* 4.5 9.9 - - + -
85D VAL* 4.1 27.1 - - + -
137D LEU* 5.9 5.2 - - + -
258D PHE* 3.6 28.5 - - + -
262D ARG* 2.9 67.0 + - + +
266D ILE* 5.3 3.4 - - + -
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Residues in contact with PHE 44 (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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40D ILE* 3.0 25.6 + - + +
41D ASN* 4.0 7.2 - - - +
43D LEU* 1.3 74.9 - - + +
45D LYS* 1.3 67.2 + - - +
70D ILE* 3.5 39.7 - - + -
72D HIS* 3.6 43.1 - + + -
74D ILE* 5.0 16.3 - - + +
83D LEU* 3.7 37.5 - - + -
85D VAL* 3.6 29.4 - - + -
262D ARG* 5.8 0.9 + - - -
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Residues in contact with LYS 45 (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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41D ASN 2.9 18.1 + - - +
42D THR* 3.4 13.3 + - - +
43D LEU 3.4 7.7 - - - +
44D PHE* 1.3 83.3 - - - +
262D ARG* 5.2 5.4 + - - -
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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