Contacts of the helix formed by residues 35 - 41 (chain A) in PDB entry 1CBM
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 TYR 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 2.9 30.1 + - + +
32A LEU 3.8 0.3 - - - +
34A VAL* 1.3 97.5 - - + +
36A PRO* 1.3 62.4 - - - +
37A TRP* 3.2 42.2 - + + -
38A THR* 2.7 39.8 + - + -
105A LEU* 3.8 31.0 - - + +
108A ASN* 5.0 8.8 + - - +
109A VAL* 3.6 25.4 - - + +
108D ASN* 5.1 2.6 + - - -
127D GLN* 5.6 1.5 + - - -
131D GLN* 3.6 30.8 + - + -
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Residues in contact with PRO 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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32A LEU 3.5 10.3 - - - +
33A VAL 4.0 7.2 - - - +
34A VAL 3.2 13.5 - - - +
35A TYR* 1.3 83.0 - - - +
37A TRP* 1.3 73.4 + - + +
38A THR 3.0 0.4 - - - -
39A GLN* 3.1 38.1 + - - +
97C HIS* 3.8 15.4 - - + +
145C TYR* 4.3 18.6 - - + -
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Residues in contact with TRP 37 (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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34A VAL 5.1 0.4 - - - -
35A TYR* 3.5 33.4 - + + -
36A PRO* 1.3 85.0 - - + +
38A THR* 1.3 73.5 + - + +
39A GLN 3.2 0.2 - - - -
40A ARG* 3.2 30.0 + - - +
102A ASN* 3.2 18.3 + - - -
105A LEU* 3.6 23.0 - - + +
97C HIS* 3.4 29.5 - - - +
99C ASP* 3.3 31.2 + - + +
100C PRO* 3.5 36.1 - - + -
145C TYR* 3.5 37.9 - + + +
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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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31A LEU* 3.5 25.6 + - + -
32A LEU* 3.4 21.3 - - - +
35A TYR* 2.7 27.3 + - + +
37A TRP* 1.3 82.0 - - + +
39A GLN* 1.3 64.2 + - - +
40A ARG 3.0 3.9 + - - -
41A PHE* 3.2 23.6 + - - -
42A PHE* 3.6 11.3 - - - -
102A ASN* 3.6 28.9 - - - +
105A LEU* 5.1 0.2 - - + -
147A HEM 4.1 12.1 - - + -
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Residues in contact with GLN 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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32A LEU* 3.0 45.0 + - + +
33A VAL* 4.8 2.4 - - - +
36A PRO* 3.1 25.1 + - - +
38A THR* 1.3 76.9 + - - +
40A ARG* 1.3 62.7 + - - +
42A PHE* 2.9 15.2 + - - +
43A GLU* 3.4 14.3 + - + +
48A LEU* 3.8 42.3 + - + +
49A SER 5.4 2.5 + - - +
54A VAL* 4.6 5.4 - - - +
97C HIS* 4.6 14.5 + - + -
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Residues in contact with ARG 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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36A PRO 4.6 0.2 + - - -
37A TRP 3.2 17.4 + - - +
38A THR 3.0 1.2 - - - -
39A GLN* 1.3 78.6 - - - +
41A PHE* 1.3 90.0 + - + +
42A PHE 3.5 0.2 + - - -
43A GLU* 4.0 28.1 + - - +
97A HIS 5.1 0.8 + - - -
99A ASP* 2.8 26.1 + - - -
37C TRP 5.8 0.6 + - - -
40C ARG* 4.0 28.2 + - - +
41C PHE* 3.3 31.0 - - - -
96C LEU 4.5 2.2 - - - +
97C HIS* 3.1 36.5 + - + -
99C ASP* 2.7 32.6 + - - -
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Residues in contact with PHE 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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38A THR* 3.2 19.0 + - - +
39A GLN 3.1 0.8 - - - -
40A ARG* 1.3 124.1 - - + +
42A PHE* 1.3 72.7 + - + +
43A GLU 3.6 1.1 - - - -
44A SER* 5.4 2.3 + - - -
45A PHE* 5.7 0.5 - - - -
96A LEU* 3.7 17.9 - - + -
97A HIS 3.9 3.4 - - - -
98A VAL* 3.7 33.9 - - + -
99A ASP* 4.0 1.3 - - - -
102A ASN* 3.8 17.3 - - - -
147A HEM 3.4 41.8 - - + +
40C ARG* 3.7 28.2 + - - +
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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