Contacts of the strand formed by residues 39 - 46 (chain D) in PDB entry 4DOH
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 GLN 39 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D ALA* 3.2 20.3 + - - +
38D PRO* 1.3 78.5 + - - +
40D GLN* 1.3 79.1 + - - +
41D LEU* 3.6 3.9 - - - +
54D TRP* 3.2 3.6 - - - -
55D SER* 2.4 47.1 + - - +
125D SER* 4.0 8.7 + - - -
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Residues in contact with GLN 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLN* 1.3 90.1 + - - +
41D LEU* 1.3 61.3 + - - +
42D SER* 4.1 2.4 + - - -
53D MET 3.1 2.8 - - - +
54D TRP* 2.9 13.9 - - - -
55D SER* 2.9 25.4 + - - +
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PRO 4.2 5.6 - - - +
39D GLN* 4.7 1.8 - - - +
40D GLN* 1.3 78.9 - - - +
42D SER* 1.3 63.8 + - - +
52D LEU* 4.3 18.2 - - + -
53D MET 2.9 6.1 - - - +
54D TRP* 4.1 11.2 - - + -
112D ARG* 5.0 2.5 - - - -
113D VAL* 3.3 33.0 - - + +
125D SER* 3.6 35.9 - - - +
126D ILE 3.9 15.3 - - - +
127D LEU* 3.9 24.5 - - + +
128D LYS* 5.2 14.4 + - + +
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Residues in contact with SER 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLN 4.8 1.6 + - - -
41D LEU* 1.3 77.5 - - - +
43D VAL* 1.3 66.9 - - - +
44D LEU 4.2 0.2 - - - -
51D LEU 3.7 0.3 - - - +
52D LEU* 3.2 5.4 - - - +
53D MET* 2.8 59.7 + - - +
127D LEU* 4.0 6.5 - - - +
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D SER* 1.3 82.8 - - - +
44D LEU* 1.3 73.7 + - - +
45D SER* 3.6 2.9 + - - -
50D HIS* 4.3 5.6 - - + -
51D LEU 3.3 16.2 - - - +
52D LEU* 4.2 17.5 - - + -
53D MET* 5.7 0.2 - - - -
99D VAL* 5.3 1.6 - - + -
111D LEU* 4.3 12.3 - - + -
127D LEU* 4.3 8.6 - - + +
131D PHE* 3.7 56.9 - - + -
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D SER 4.2 0.4 - - - -
43D VAL* 1.3 75.4 - - - +
45D SER* 1.3 62.2 + - - +
46D THR* 4.1 6.6 + - + +
49D LYS 3.6 3.5 - - - +
51D LEU* 2.7 49.0 + - + +
53D MET* 4.0 29.0 - - + +
137D ILE* 6.1 3.1 - - + -
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL 3.6 3.2 + - - -
44D LEU* 1.3 76.2 - - - +
46D THR* 1.3 55.6 + - - +
49D LYS 3.2 4.5 + - - -
50D HIS* 2.8 28.3 + - - -
131D PHE* 3.6 22.4 - - - -
135D SER 5.1 0.9 - - - -
136D THR* 2.6 33.6 + - - -
137D ILE* 2.7 38.4 + - - +
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Residues in contact with THR 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 4.1 8.7 + - + +
45D SER* 1.3 74.7 - - - +
47D ASN* 1.3 75.0 - - - +
48D MET 3.3 2.2 - - - -
49D LYS* 3.1 24.1 + - - +
137D ILE* 3.4 34.3 - - + +
139D THR* 5.7 4.7 - - - +
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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