Contacts of the strand formed by residues 35 - 40 (chain L) in PDB entry 3KDM
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 VAL 35 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22L CYS* 4.9 2.7 - - - -
29L VAL* 3.9 41.1 - - + +
32L TYR 4.6 4.0 - - - +
33L ASN 3.6 2.6 - - - -
34L TYR* 1.3 78.9 - - - +
36L SER* 1.3 68.4 + - - +
37L TRP* 4.0 12.6 - - + +
50L ILE* 4.4 1.6 - - - +
51L TYR* 3.5 1.4 - - - -
52L GLY 3.2 5.7 + - - -
53L VAL* 2.8 46.0 + - + +
68L LYS* 5.1 0.2 - - + -
73L ALA* 3.7 23.3 - - + -
90L CYS* 4.4 7.6 - - + -
91L SER 3.2 11.7 - - - +
92L SER* 4.5 2.0 - - - +
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Residues in contact with SER 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H TYR 4.4 0.2 + - - -
107H TYR 2.8 24.7 + - - -
108H GLY* 3.6 3.5 - - - -
34L TYR 3.9 1.2 + - - -
35L VAL* 1.3 72.9 - - - +
37L TRP* 1.3 64.5 + - - +
38L TYR* 4.0 5.4 - - - -
48L LEU* 3.9 11.2 - - - -
50L ILE 3.1 9.4 - - - -
51L TYR* 3.5 16.1 - - - +
52L GLY 4.3 1.4 + - - -
90L CYS* 3.0 8.4 - - - +
91L SER* 2.8 46.2 + - - -
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Residues in contact with TRP 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L GLN* 3.8 10.5 - - - -
20L ILE* 3.5 37.5 - - + -
21L SER 4.1 0.7 - - - -
22L CYS* 3.5 31.9 - - + -
35L VAL* 4.0 13.0 - - + +
36L SER* 1.3 77.4 - - - +
38L TYR* 1.3 58.8 + - - +
48L LEU* 3.7 4.3 - - - +
49L MET* 2.7 33.0 + - + -
50L ILE* 2.8 42.9 + - + +
53L VAL 4.8 2.9 + - - -
66L GLY* 4.9 1.2 - - - -
67L SER 5.2 0.2 + - - -
73L ALA* 3.8 12.2 - - + +
74L SER* 4.0 10.9 + - - -
75L LEU* 3.5 47.3 - - + -
88L TYR* 4.7 3.6 - - + -
89L TYR 3.3 10.5 - - - -
90L CYS* 3.7 25.6 - - + -
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Residues in contact with TYR 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H LEU* 5.0 1.6 - - + -
108H GLY* 3.4 4.3 - - - -
109H MET* 2.9 46.3 + - + +
112H TRP* 3.8 18.4 - + - -
36L SER* 4.0 7.0 - - - -
37L TRP* 1.3 77.3 - - - +
39L GLN* 1.3 59.2 + - - +
40L GLN 4.1 0.2 - - - -
46L PRO* 4.1 14.6 - - + -
47L LYS 3.1 17.5 - - - +
48L LEU* 3.6 17.9 - - + -
49L MET* 4.1 2.5 - - - -
87L ASP 3.8 0.2 - - - +
88L TYR* 3.2 11.2 - - - +
89L TYR* 2.7 49.8 + - + +
91L SER* 3.7 10.8 - - - -
100L TYR* 2.9 28.7 + - - -
102L PHE* 3.6 24.9 - + - -
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Residues in contact with GLN 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L TYR* 1.3 73.0 - - - +
40L GLN* 1.3 63.3 + - - +
41L HIS* 3.2 31.9 + - + +
45L ALA 4.3 0.7 - - - +
46L PRO* 3.4 0.8 - - - +
47L LYS* 2.8 48.1 + - + +
49L MET* 3.6 20.9 - - + +
64L PHE* 3.9 15.2 - - - -
83L GLY 4.9 0.2 + - - -
84L ASP* 4.5 4.9 + - - +
86L ALA* 3.7 11.0 - - + -
87L ASP 3.6 3.4 - - - -
88L TYR* 2.7 41.3 + - + -
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Residues in contact with GLN 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLN* 3.0 41.7 + - - -
45H LEU* 3.8 2.3 - - - +
95H TYR* 3.6 9.5 + - - -
39L GLN* 1.3 75.7 - - - +
41L HIS* 1.3 66.2 + - - +
42L PRO* 4.0 0.5 - - - +
43L GLY 5.9 1.0 - - - +
44L LYS 3.0 28.2 + - - +
45L ALA 4.2 0.9 - - - -
46L PRO* 3.7 30.0 - - + +
86L ALA* 3.3 4.1 - - - +
87L ASP* 2.8 47.5 + - + +
89L TYR* 3.7 20.1 + - + -
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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