Contacts of the strand formed by residues 70 - 75 (chain D) in PDB entry 3SDL
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 THR 70 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D THR* 3.2 27.8 - - + +
8D LYS* 3.9 26.2 - - + -
14D GLU* 4.4 6.6 + - - +
47D VAL* 4.4 0.7 - - - +
48D HIS* 3.1 55.7 + - + +
65D LEU* 4.5 3.2 - - - +
68D GLY 4.3 4.3 + - - -
69D SER* 1.3 79.0 + - - +
71D VAL* 1.3 66.9 + - - +
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Residues in contact with VAL 71 (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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5D LEU* 3.8 22.0 - - + -
6D THR 2.7 17.9 + - - +
7D VAL* 3.3 21.6 - - + +
8D LYS 2.8 31.9 + - - -
28D LEU* 4.5 9.2 - - + -
45D LEU* 4.8 8.1 - - + -
46D ALA 3.4 11.2 - - - +
54D LEU* 4.2 12.1 - - + -
65D LEU* 3.7 39.3 - - + -
70D THR* 1.3 73.4 - - - +
72D LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PRO* 4.3 24.0 - - + +
98B GLU* 4.9 8.3 - - - +
8D LYS* 3.3 30.7 - - + +
9D MET 6.0 0.2 - - - +
44D ARG 3.4 1.2 - - - +
45D LEU* 3.2 11.1 - - - +
46D ALA* 2.7 43.3 + - + +
47D VAL 3.7 16.2 - - - +
48D HIS* 3.6 35.2 - - + +
49D PRO* 5.2 0.9 - - + -
51D GLY* 4.5 8.7 - - - +
71D VAL* 1.3 73.1 - - - +
73D LEU* 1.3 59.9 + - - +
74D VAL* 4.1 0.9 - - + -
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Residues in contact with LEU 73 (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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37A GLN* 4.4 1.6 - - - +
7D VAL* 3.7 21.3 - - + -
8D LYS 2.8 10.9 + - - +
9D MET* 3.6 36.5 - - + +
10D LEU 3.9 5.5 + - - -
32D ILE* 4.0 13.2 - - + -
36D ILE* 3.8 28.9 - - + -
38D VAL* 5.1 0.9 - - + -
43D GLN* 3.8 29.6 - - + +
44D ARG 3.6 1.6 - - - +
45D LEU* 3.6 19.1 - - + -
71D VAL 3.9 0.4 + - - -
72D LEU* 1.3 72.7 - - - +
74D VAL* 1.3 78.5 - - - +
75D VAL* 4.4 9.1 + - + -
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Residues in contact with VAL 74 (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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37A GLN* 3.7 10.5 - - - +
87B VAL* 5.0 13.0 - - + +
88B LEU* 5.2 3.6 - - + -
91B MET* 3.5 39.3 - - + -
92B ASP 4.6 0.7 - - - +
93B PRO* 3.5 39.3 - - + -
10D LEU* 5.5 8.5 - - + -
42D GLN 3.7 0.2 - - - +
44D ARG* 2.9 43.7 + - + +
72D LEU* 5.8 0.9 - - + -
73D LEU* 1.3 80.2 - - - +
75D VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 75 (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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36A TRP* 3.6 33.7 - - + +
37A GLN* 2.8 42.9 + - - +
91B MET* 3.0 9.3 - - - +
9D MET* 3.8 21.3 - - + -
38D VAL* 3.9 37.2 - - + -
42D GLN* 3.6 14.6 - - + +
43D GLN* 5.2 0.2 - - - +
73D LEU* 4.4 6.5 - - + -
74D VAL* 1.3 73.7 - - - +
76D ASP* 1.3 65.3 + - - +
77D LYS* 4.6 1.6 - - - +
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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