Contacts of the helix formed by residues 40 - 52 (chain A) in PDB entry 4B23
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 ALA 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLU 3.5 3.4 + - - -
39A HIS* 1.3 74.7 - - - +
41A PRO* 1.3 77.3 - - + +
42A TYR* 3.3 30.5 - - + -
43A GLU* 3.0 17.4 + - + +
44A GLY* 3.0 10.7 + - - -
118A LYS* 4.1 6.3 - - - +
147A TYR* 5.0 0.2 - - - -
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Residues in contact with PRO 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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40A ALA* 1.3 85.5 - - + +
42A TYR* 1.3 57.3 + - - +
44A GLY* 3.2 1.2 + - - -
45A ILE* 2.8 38.7 + - + +
115A ILE* 4.2 16.6 - - + -
116A PRO 4.1 2.9 - - - +
117A SER* 5.2 0.2 - - - -
118A LYS* 3.9 34.3 - - + +
121A ILE* 3.7 22.9 - - + -
147A TYR* 3.4 26.6 - - + +
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Residues in contact with TYR 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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40A ALA* 3.3 25.2 - - + -
41A PRO* 1.3 79.2 - - + +
43A GLU* 1.3 63.7 + - + +
45A ILE* 3.8 2.6 - - - +
46A ILE* 3.0 46.7 + - + +
76A PHE* 3.8 23.5 + + - +
77A PRO 2.7 29.0 + - - -
78A THR* 3.4 10.0 - - - +
79A PRO* 3.5 33.5 - - + +
82A ILE* 4.2 6.3 - - + -
106A VAL* 4.1 16.1 - - + +
107A ALA* 5.3 1.8 - - - -
110A ALA* 3.6 26.7 - - + -
115A ILE* 4.2 6.1 - - + +
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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 HIS* 3.1 34.0 + - + +
40A ALA* 3.0 14.8 + - - +
42A TYR* 1.3 87.6 + - + +
44A GLY* 1.3 66.7 + - - +
46A ILE* 3.2 2.6 + - - +
47A ARG* 2.8 57.4 + - - +
76A PHE* 3.3 53.6 - - + +
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Residues in contact with GLY 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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39A HIS* 4.5 2.8 - - - +
40A ALA 3.0 11.4 + - - -
41A PRO 3.7 2.2 - - - -
43A GLU* 1.3 76.2 - - - +
45A ILE* 1.3 62.8 + - - +
47A ARG* 3.3 9.2 + - - +
48A ALA* 3.0 23.7 + - - +
147A TYR* 3.7 14.5 - - - +
151A THR* 3.3 26.1 + - - -
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Residues in contact with ILE 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 PRO* 2.8 32.2 + - + +
42A TYR* 3.8 6.1 - - - +
44A GLY* 1.3 72.5 - - - +
46A ILE* 1.3 59.0 + - - +
48A ALA* 3.1 7.0 + - - +
49A ILE* 2.8 50.2 + - + +
106A VAL* 4.2 13.7 - - + -
115A ILE* 4.4 13.9 - - + -
121A ILE* 5.9 0.2 - - + -
133A LEU* 4.2 21.8 - - + -
136A ILE* 4.2 21.3 - - + -
139A VAL* 3.9 18.8 - - + -
143A THR* 5.5 1.3 - - + -
147A TYR* 3.9 16.8 - - + -
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Residues in contact with ILE 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 TYR* 3.0 33.5 + - + +
43A GLU 3.7 3.4 - - - +
45A ILE* 1.3 75.1 - - - +
47A ARG* 1.3 61.6 + - - +
49A ILE* 3.3 8.2 + - + +
50A THR* 2.8 34.3 + - - +
63A ILE* 5.1 1.6 - - + -
66A PHE* 4.6 6.5 - - + -
76A PHE* 4.0 18.4 - - + -
82A ILE* 3.7 24.7 - - + -
95A PHE* 4.8 1.6 - - + -
103A ILE* 3.7 50.5 - - + +
106A VAL* 3.9 17.3 - - + -
107A ALA 5.0 0.9 - - - +
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Residues in contact with ARG 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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39A HIS* 3.5 24.1 + - - -
43A GLU* 2.8 50.7 + - - +
44A GLY* 3.6 7.2 - - - +
46A ILE* 1.3 75.9 - - - +
48A ALA* 1.3 63.5 + - - +
50A THR* 3.5 7.2 + - - -
51A SER* 3.2 21.7 + - - -
59A THR* 4.5 4.7 - - + +
60A ASN* 5.8 1.8 + - - -
63A ILE* 4.0 29.9 - - + +
67A CYS* 5.1 3.2 - - - -
76A PHE* 3.9 25.2 - - + +
151A THR* 5.4 2.0 - - - +
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Residues in contact with ALA 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 GLY 3.0 16.8 + - - +
45A ILE* 3.1 5.6 + - - +
47A ARG* 1.3 75.5 - - - +
49A ILE* 1.3 65.6 + - - +
51A SER* 2.8 24.5 + - - -
52A GLN* 3.6 8.1 + - - +
142A TRP* 3.9 3.1 - - - -
143A THR* 3.5 31.8 - - + +
146A MET* 4.4 7.2 - - + -
147A TYR* 4.3 14.4 - - + +
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Residues in contact with ILE 49 (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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45A ILE* 2.8 29.3 + - + +
46A ILE* 3.3 7.8 + - - +
48A ALA* 1.3 75.1 - - - +
50A THR* 1.3 65.6 + - - +
52A GLN* 3.1 34.6 + - - +
99A LYS* 3.3 29.0 - - + +
102A GLU* 4.1 23.8 - - + +
103A ILE* 4.5 14.4 - - + -
106A VAL* 4.1 15.9 - - + -
137A LYS 4.8 0.9 - - - +
138A GLY 4.1 7.0 - - - +
139A VAL* 3.8 29.8 - - + -
143A THR* 4.2 3.1 - - + -
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Residues in contact with THR 50 (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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46A ILE 2.8 20.9 + - - -
47A ARG 3.7 5.2 - - - -
48A ALA 3.3 0.2 - - - -
49A ILE* 1.3 78.0 - - - +
51A SER* 1.3 56.1 + - - +
54A LEU* 3.4 9.9 - - + +
59A THR* 3.8 19.5 + - + -
62A ILE* 4.2 20.2 - - + -
63A ILE* 3.8 13.6 - - + +
95A PHE* 3.1 38.2 - - + -
99A LYS* 2.7 30.6 + - + +
103A ILE* 4.1 2.1 - - - +
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Residues in contact with SER 51 (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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47A ARG 3.2 9.8 + - - -
48A ALA* 2.8 23.8 + - - -
49A ILE 3.2 0.2 - - - -
50A THR* 1.3 76.0 - - - +
52A GLN* 1.3 65.2 + - - +
53A LYS 3.1 1.2 + - - -
54A LEU 3.0 21.9 + - - +
56A ASP* 5.7 4.3 - - - -
59A THR* 3.4 22.2 - - - +
142A TRP* 3.4 22.1 - - - -
146A MET* 4.8 4.0 - - - +
7X A 4.0 0.9 + - - -
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Residues in contact with GLN 52 (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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48A ALA 3.8 6.3 - - - +
49A ILE* 3.1 32.5 + - - +
50A THR 3.2 0.4 - - - -
51A SER* 1.3 75.2 + - - +
53A LYS* 1.3 65.4 + - + +
54A LEU* 3.0 5.8 + - - +
99A LYS* 2.8 36.5 + - - +
102A GLU* 4.9 2.9 - - - +
138A GLY 2.8 22.9 + - - +
142A TRP* 3.8 17.7 - - + -
143A THR* 2.7 24.8 + - - +
7X A 3.4 21.3 + - - +
8X A 3.4 21.0 - - - +
16Y T 4.4 0.3 + - - -
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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