Contacts of the helix formed by residues 37 - 47 (chain A) in PDB entry 4BEJ
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLN 4.0 6.5 + - - -
35A SER 3.1 6.3 - - - -
36A SER* 1.3 79.6 - - - +
38A LYS* 1.3 64.0 + - - +
39A SER* 3.2 4.5 - - - -
40A SER* 2.3 35.6 + - - -
41A VAL* 3.2 7.9 + - - +
215A THR* 5.5 0.4 - - - -
216A LYS* 5.1 4.7 - - - -
246A ASN* 4.1 0.3 + - - -
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Residues in contact with LYS 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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30A VAL* 2.6 41.2 + - + -
31A VAL* 3.5 1.0 - - - +
32A GLY* 3.2 36.6 + - - +
33A THR 4.4 6.1 - - - +
34A GLN* 5.2 3.7 + - - +
36A SER* 3.3 3.7 - - - -
37A GLY* 1.3 75.4 - - - +
39A SER* 1.3 71.1 + - - +
41A VAL* 3.2 12.9 + - - +
42A LEU* 3.2 26.9 + - - +
146A ASP* 3.2 21.9 + - - +
147A LEU 3.1 19.5 + - - +
148A PRO 5.0 0.6 + - - -
149A GLY* 4.9 5.6 - - - +
184A VAL* 4.6 17.9 - - + -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY* 3.2 1.7 - - - -
38A LYS* 1.3 84.3 - - - +
40A SER* 1.3 58.0 + - - +
42A LEU* 3.2 3.5 + - - +
43A GLU* 2.9 38.1 + - - +
51A LEU* 3.3 42.1 - - - +
52A PRO 4.8 1.7 + - - -
53A ARG* 6.1 1.1 - - - -
146A ASP* 5.6 0.2 + - - -
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY* 2.3 30.5 + - - -
39A SER* 1.3 78.1 - - - +
41A VAL* 1.3 54.1 + - - +
43A GLU* 3.6 12.1 + - - +
44A SER* 2.8 36.2 + - - -
53A ARG* 5.8 3.6 - - - +
246A ASN* 2.9 33.1 + - - +
247A ARG* 4.0 17.6 + - - -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 5.9 1.1 - - + -
37A GLY 3.4 13.9 - - - +
38A LYS* 3.3 15.5 - - + +
40A SER* 1.3 77.1 + - - +
42A LEU* 1.3 68.0 + - + +
44A SER* 3.3 3.9 + - - -
45A LEU* 3.2 29.7 + - + +
182A LEU* 5.2 8.7 - - + -
184A VAL* 4.1 13.7 - - + -
213A VAL* 4.9 7.4 - - + -
215A THR* 3.6 17.9 - - + -
244A VAL* 5.0 1.8 - - + -
246A ASN* 3.6 19.5 - - - +
285A LEU* 4.4 22.4 - - + +
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Residues in contact with LEU 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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30A VAL* 4.4 17.7 - - + -
38A LYS 3.2 13.1 + - - +
39A SER* 3.6 5.2 - - - +
41A VAL* 1.3 84.1 - - + +
43A GLU* 1.3 63.1 + - + +
45A LEU* 3.1 19.7 + - + +
46A VAL* 3.3 14.9 + - - +
51A LEU* 3.7 20.2 - - + -
63A LEU* 5.3 3.1 - - + -
65A LEU* 4.5 23.9 - - + +
144A LEU* 3.8 31.4 - - + -
146A ASP* 3.5 39.9 - - + +
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Residues in contact with GLU 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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39A SER* 2.9 24.4 + - - +
40A SER* 3.8 10.2 - - - +
42A LEU* 1.3 77.4 - - + +
44A SER* 1.3 57.7 + - - +
46A VAL* 3.2 9.1 - - - +
47A GLY 3.0 22.2 + - - -
48A ARG 3.5 17.3 + - - +
49A ASP* 2.9 25.5 - - - +
50A LEU* 3.2 3.9 + - + +
51A LEU* 3.0 45.9 + - + +
53A ARG* 3.1 24.1 + - - -
247A ARG* 3.9 2.9 + - - +
258A VAL* 3.6 11.7 - - + +
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Residues in contact with SER 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 SER 2.8 17.4 + - - -
41A VAL* 3.8 4.9 - - - -
42A LEU 3.2 0.4 - - - -
43A GLU* 1.3 75.2 - - - +
45A LEU* 1.3 65.0 + - - +
47A GLY* 3.9 5.6 + - - -
245A VAL 5.7 0.3 + - - -
246A ASN* 4.1 14.3 + - - +
258A VAL* 3.9 10.1 - - - -
262A ILE* 3.3 23.0 - - - +
282A THR* 3.0 38.5 + - - +
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Residues in contact with LEU 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 VAL* 3.2 24.3 + - + +
42A LEU* 3.1 14.5 + - + +
44A SER* 1.3 82.5 - - - +
46A VAL* 1.3 62.2 + - - +
47A GLY* 4.5 0.2 - - - -
65A LEU* 6.3 0.7 - - + -
67A LEU* 4.1 15.9 - - + +
138A ASN 4.7 3.1 - - - +
139A VAL* 3.7 14.8 - - - +
140A VAL* 5.9 0.2 - - + -
142A LEU* 4.1 12.1 - - + -
144A LEU* 3.6 31.9 - - + -
282A THR* 4.7 6.5 - - + +
285A LEU* 4.8 8.3 - - + -
286A ALA* 4.0 37.5 - - + +
289A LEU* 4.4 12.1 - - + -
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Residues in contact with VAL 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 LEU 3.3 11.7 - - - +
43A GLU* 3.2 15.7 - - - +
45A LEU* 1.3 79.7 - - - +
47A GLY* 1.3 62.1 + - - +
48A ARG* 3.4 27.3 - - + +
50A LEU* 3.4 29.6 - - + -
65A LEU* 5.4 2.9 - - + -
67A LEU* 4.3 13.9 - - + +
89A GLU* 4.6 6.2 - - - +
104A PHE* 4.9 0.2 - - + -
134A ILE* 4.0 25.6 - - + -
136A SER* 4.7 1.4 + - - -
138A ASN* 5.1 3.5 - - - +
139A VAL* 3.1 24.6 - - + +
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Residues in contact with GLY 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 GLU 3.0 10.2 + - - -
44A SER 3.9 3.8 + - - -
45A LEU 3.3 2.8 - - - -
46A VAL* 1.3 77.6 - - - +
48A ARG* 1.3 73.0 + - - +
89A GLU* 5.1 1.9 - - - +
138A ASN* 6.1 2.7 - - - -
258A VAL* 3.7 23.4 - - - +
259A THR* 4.1 13.6 + - - -
262A ILE* 6.3 2.5 - - - -
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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