Contacts of the helix formed by residues 35 - 48 (chain A) in PDB entry 5CYO
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLY 3.4 1.6 + - - -
34A LEU* 1.3 80.2 - - - +
36A LYS* 1.3 58.6 + - - +
37A SER 3.5 2.2 - - - -
38A THR* 3.4 1.9 + - - -
39A LEU* 2.9 30.8 + - - +
139A PHE* 4.0 2.5 - - - -
170A LYS* 4.1 1.0 - - - +
226A GLY* 5.5 0.3 - - - -
301A GDP 2.9 49.0 + - - -
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Residues in contact with LYS 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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28A VAL* 3.9 14.1 - - + +
29A VAL 3.6 13.7 - - - +
30A GLY* 3.3 37.6 + - - +
31A GLN 2.8 24.0 + - - -
32A SER* 3.6 5.9 + - - +
34A LEU* 4.4 2.7 - - + -
35A GLY* 1.3 75.1 - - - +
37A SER* 1.3 67.0 + - - +
39A LEU* 3.2 4.2 + - - +
40A ILE* 3.1 26.5 + - - +
64A THR* 6.3 0.2 - - - -
87A ASP* 4.6 1.6 - - - +
88A THR* 4.0 25.2 + - - -
90A GLY* 4.9 1.0 - - - +
139A PHE* 3.6 32.7 - - + -
301A GDP 2.7 34.4 + - - +
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 1.3 75.9 - - - +
38A THR* 1.3 62.3 + - - +
40A ILE* 3.4 14.7 + - - +
41A ASN* 3.4 9.9 + - - +
61A ILE* 3.7 32.1 - - - +
64A THR* 2.7 3.1 + - - -
68A LYS* 5.4 0.9 - - - -
87A ASP* 2.5 27.9 + - - -
301A GDP 2.9 11.1 + - - -
302A MG 2.1 30.6 - - - -
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Residues in contact with THR 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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35A GLY 3.5 6.5 - - - -
36A LYS 3.2 0.2 - - - -
37A SER* 1.3 78.6 - - - +
39A LEU* 1.3 57.8 + - - +
41A ASN* 3.2 7.4 + - - +
42A THR* 3.0 26.7 + - - -
61A ILE* 3.8 15.2 - - + +
226A GLY* 3.9 11.2 - - - -
227A SER 3.4 24.2 - - - +
228A ASP* 5.6 1.6 - - + -
301A GDP 2.7 62.4 + - + +
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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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35A GLY 2.9 18.1 + - - +
36A LYS 3.2 4.9 + - - +
38A THR* 1.3 73.6 - - - +
40A ILE* 1.3 60.1 + - - +
42A THR* 3.5 4.2 - - - -
43A LEU* 2.8 30.1 + - + +
137A LEU* 4.7 7.4 - - + -
139A PHE* 3.5 26.0 - - + -
167A VAL* 5.2 1.3 - - + -
224A VAL* 3.8 23.1 - - + -
225A VAL 3.8 25.4 - - - +
226A GLY* 3.9 9.0 - - - +
258A PHE* 3.9 22.0 - - + -
261A LEU* 4.3 19.5 - - + -
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Residues in contact with ILE 40 (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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28A VAL* 3.9 15.7 - - + +
36A LYS 3.1 13.6 + - - +
37A SER* 3.4 7.6 - - - +
39A LEU* 1.3 76.5 - - - +
41A ASN* 1.3 62.7 + - - +
43A LEU* 3.2 7.5 + - - +
44A PHE* 3.1 47.4 + - + -
70A ILE* 3.9 18.6 - - + -
85A VAL* 3.6 29.8 - - + -
87A ASP* 3.5 45.3 - - + +
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Residues in contact with ASN 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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37A SER 3.4 7.9 + - - +
38A THR* 3.2 11.5 + - + +
40A ILE* 1.3 80.8 - - - +
42A THR* 1.3 62.7 + - - +
44A PHE* 3.6 6.8 + - - +
45A LYS* 3.1 44.6 + - - +
58A GLU* 2.9 33.2 + - - +
61A ILE* 5.2 7.4 - - + -
227A SER* 5.0 3.5 + - - +
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Residues in contact with THR 42 (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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38A THR 3.0 12.9 + - - -
39A LEU* 3.2 15.7 + - + -
41A ASN* 1.3 77.3 - - - +
43A LEU* 1.3 56.6 + - - +
45A LYS* 3.3 5.4 + - - +
46A SER* 2.9 27.0 + - - -
225A VAL 4.6 0.7 - - - +
226A GLY* 3.7 1.2 - - - -
227A SER* 2.9 43.5 + - - +
239A LEU* 3.7 5.1 - - + +
250A VAL* 4.0 17.9 - - + -
258A PHE* 3.6 28.3 - - + -
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Residues in contact with LEU 43 (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 ILE* 3.9 16.4 - - + -
39A LEU* 2.8 21.7 + - + +
40A ILE* 3.6 6.1 - - - +
42A THR* 1.3 74.6 - - - +
44A PHE* 1.3 61.8 + - - +
46A SER* 2.7 28.4 + - - +
47A LYS* 3.4 28.8 + - - +
83A LEU* 4.5 9.2 - - + -
85A VAL* 4.4 17.7 - - + -
137A LEU* 5.2 9.0 - - + -
258A PHE* 3.9 17.7 - - + -
261A LEU* 5.7 1.8 - - + -
262A ARG* 4.6 5.2 - - - -
265A LEU* 3.8 29.2 - - + -
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Residues in contact with PHE 44 (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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40A ILE* 3.1 33.8 + - + +
41A ASN* 4.0 7.0 - - - +
42A THR 3.4 0.2 - - - -
43A LEU* 1.3 77.1 - - - +
45A LYS* 1.3 59.5 + - + +
47A LYS* 3.2 3.1 + - - -
48A ILE* 2.9 42.6 + - + +
70A ILE* 3.4 39.7 - - + -
72A HIS* 3.6 37.9 - + + -
74A ILE* 4.7 3.4 - - + -
83A LEU* 3.4 38.8 - - + -
85A VAL* 3.5 26.2 - - + -
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Residues in contact with LYS 45 (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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41A ASN* 3.1 47.2 + - - +
42A THR* 3.7 4.3 - - - +
44A PHE* 1.3 77.0 - - + +
46A SER* 1.3 62.7 + - - +
47A LYS 3.1 1.3 + - - -
48A ILE* 3.2 9.1 - - - +
58A GLU* 3.1 28.3 + - - +
227A SER* 5.3 2.2 - - - +
230A GLU* 3.3 22.9 - - - +
237A ARG* 2.8 43.0 + - - +
239A LEU* 3.9 21.9 - - + +
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Residues in contact with SER 46 (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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42A THR 2.9 14.8 + - - -
43A LEU* 2.7 23.0 + - - +
44A PHE 3.2 0.4 - - - -
45A LYS* 1.3 76.2 - - - +
47A LYS* 1.3 68.1 + - - +
48A ILE 5.2 0.4 - - - -
239A LEU* 3.9 7.8 - - - +
251A GLU* 3.6 22.5 - - - +
258A PHE* 3.7 16.1 - - - -
262A ARG* 3.6 21.0 - - - +
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Residues in contact with LYS 47 (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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43A LEU* 3.4 24.7 + - + +
44A PHE* 3.2 2.9 + - - +
45A LYS 3.1 0.4 - - - -
46A SER* 1.3 89.5 + - - +
48A ILE* 1.3 65.1 + - - +
49A SER* 3.9 2.8 + - - -
74A ILE* 3.8 42.3 - - + +
75A GLU 4.3 12.6 + - - +
76A GLU* 5.7 1.2 + - - -
83A LEU* 4.7 7.6 - - + -
262A ARG* 2.9 36.0 + - - +
263A ASP* 5.6 0.2 + - - -
265A LEU* 3.1 33.3 + - - +
266A ILE* 4.1 9.7 - - - +
270A MET* 5.1 0.7 - - + -
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Residues in contact with ILE 48 (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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44A PHE* 2.9 26.8 + - + +
45A LYS* 3.2 4.7 + - - +
46A SER 5.2 0.2 - - - -
47A LYS* 1.3 80.3 - - - +
49A SER* 1.3 68.6 + - - +
50A ARG* 4.4 1.7 - - + +
72A HIS* 3.9 31.6 - - + +
73A ASP 3.9 11.4 - - - +
74A ILE* 3.7 16.6 - - + -
237A ARG* 2.9 23.7 + - - -
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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