Contacts of the helix formed by residues 38 - 44 (chain A) in PDB entry 3SPD
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 LEU 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ARG 5.0 0.4 + - - -
36A ASP 3.1 1.2 - - - -
37A ASN* 1.3 76.7 - - + +
39A LYS* 1.3 66.3 + - - +
40A VAL 3.1 3.1 - - - -
41A TYR* 3.0 36.7 + - + +
42A ILE 3.9 0.3 + - - -
73A LEU* 4.2 18.2 - - + -
75A MET* 3.5 26.4 - - + +
143A MET* 3.7 36.3 - - + -
145A ASN* 4.1 10.7 - - + +
147A HIS* 3.6 41.3 - - + +
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP* 3.1 26.4 + - + +
38A LEU* 1.3 78.5 - - - +
40A VAL* 1.3 70.9 + - + +
41A TYR 3.1 0.5 + - - -
42A ILE* 3.2 10.4 + - + +
43A GLU* 3.0 29.7 + - + +
145A ASN* 3.3 29.7 - - - +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP 5.5 0.7 - - - +
37A ASN 3.7 18.2 - - - +
39A LYS* 1.3 88.3 - - + +
41A TYR* 1.3 71.7 + - + +
43A GLU* 3.9 5.8 - - - +
44A SER* 2.9 31.5 + - - -
48A TYR* 3.3 36.9 - - + +
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Residues in contact with TYR 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 ASN 4.6 2.2 - - - -
38A LEU* 3.0 44.9 + - + +
40A VAL* 1.3 89.9 - - + +
42A ILE* 1.3 62.3 + - - +
45A PRO* 3.3 27.5 - - - +
48A TYR* 3.7 43.5 - + + -
50A ASN* 5.8 2.7 - - + -
51A VAL* 3.9 10.5 - - + -
59A VAL* 3.5 10.5 - - + +
61A VAL* 3.8 34.3 - - + -
62A ARG 5.3 3.2 + - - -
64A MET* 4.8 19.3 - - + +
73A LEU* 6.2 0.2 - - + -
75A MET* 4.3 10.8 - - - -
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Residues in contact with ILE 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 LEU 3.9 0.8 + - - +
39A LYS* 3.3 19.5 - - + +
41A TYR* 1.3 79.0 - - - +
43A GLU* 1.3 60.6 + - + +
59A VAL* 4.1 7.0 - - + -
75A MET* 3.6 30.3 - - + +
76A THR 3.3 24.2 - - - +
77A ARG* 2.9 50.5 + - + +
79A PRO* 6.3 0.4 - - + -
82A THR* 3.5 32.8 - - + +
145A ASN* 3.7 13.7 - - + +
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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 LYS* 3.0 24.3 + - + +
40A VAL* 4.3 3.8 - - - +
42A ILE* 1.3 81.5 - - + +
44A SER* 1.3 68.1 + - - +
45A PRO* 3.5 4.9 - - - +
46A GLU* 4.2 4.5 - - - +
77A ARG* 3.8 6.3 + - - +
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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 VAL* 2.9 15.4 + - - -
43A GLU* 1.3 90.6 + - - +
45A PRO* 1.3 66.4 - - - +
46A GLU* 3.0 15.2 + - - -
47A SER* 2.9 28.0 + - - -
48A TYR* 3.2 15.3 - - - -
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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