Contacts of the strand formed by residues 38 - 43 (chain L) in PDB entry 1A4J
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L MET* 4.1 13.9 - - + -
23L CYS* 4.1 8.3 - - - -
29L LEU* 3.4 27.1 - - + -
36L THR* 2.9 10.0 + - + +
37L TYR* 1.3 72.3 - - - +
39L HIS* 1.3 61.8 + - - +
40L TRP* 3.6 30.9 - - + +
53L ILE 4.5 0.3 - - - +
55L LYS* 3.3 2.6 + - - +
56L VAL* 2.7 36.0 + - + -
76L PHE* 3.5 47.8 - - + -
93L CYS* 4.5 0.2 - - + -
94L SER 3.3 17.5 - - - +
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Residues in contact with HIS 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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103H ARG 3.3 10.0 + - - -
104H ARG 3.0 27.1 + - - -
105H THR* 3.1 29.2 - - + +
37L TYR* 3.7 24.0 - - + -
38L LEU* 1.3 73.5 - - - +
40L TRP* 1.3 63.7 + - - +
41L TYR* 3.7 27.2 + - + +
51L LEU* 4.3 2.5 - - + -
53L ILE 3.1 11.2 - - - +
54L TYR* 3.2 2.9 - - - +
55L LYS* 3.1 30.4 + - - +
92L PHE 4.0 0.2 - - - +
93L CYS* 3.2 5.4 - - - +
94L SER* 2.8 42.6 + - - -
96L SER* 3.8 8.3 - - - -
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Residues in contact with TRP 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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6L GLN* 4.2 6.1 - - - -
21L ILE* 3.5 38.6 - - + -
23L CYS* 3.3 31.4 - - + -
38L LEU* 3.6 15.8 - - + +
39L HIS* 1.3 76.3 - - - +
41L TYR* 1.3 58.2 + - - +
51L LEU* 3.8 1.0 - - - +
52L LEU* 2.8 34.8 + - + +
53L ILE* 2.7 42.7 + - + +
56L VAL 4.7 5.1 + - - -
69L GLY* 5.2 0.4 - - - -
70L SER 5.3 0.2 + - - -
76L PHE* 4.1 9.7 - - + +
77L THR* 4.0 8.3 + - - -
78L LEU* 3.6 52.6 - - + +
91L TYR* 4.9 1.6 - - + -
92L PHE 3.3 10.8 - - - -
93L CYS* 3.5 29.2 - - + -
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Residues in contact with TYR 41 (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* 6.2 0.7 - - + -
105H THR* 4.0 3.8 - - - -
106H PHE* 3.1 59.1 + + + +
109H TRP* 3.7 20.4 - + - -
39L HIS* 3.7 27.1 + - + +
40L TRP* 1.3 78.2 - - - +
42L LEU* 1.3 60.0 + - - +
49L PRO* 4.4 8.1 - - + -
50L LYS 3.2 12.1 - - - +
51L LEU* 3.6 25.6 - - + -
52L LEU* 4.4 3.8 - - - +
91L TYR* 3.2 8.3 - - - +
92L PHE* 2.7 53.9 + - + +
94L SER* 3.5 28.1 + - - -
103L PHE* 4.5 6.3 - + - -
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Residues in contact with LEU 42 (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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41L TYR* 1.3 74.3 - - - +
43L GLN* 1.3 69.9 + - - +
44L LYS* 4.2 23.7 + - + +
48L SER 4.4 0.7 - - - +
49L PRO* 3.6 0.6 - - - +
50L LYS* 2.9 35.8 + - + +
52L LEU* 3.7 27.7 - - + +
67L PHE* 5.2 3.6 - - + -
86L GLU 4.4 10.1 - - - +
87L ASP* 4.3 6.5 - - - +
89L GLY* 3.8 11.0 - - - +
90L VAL 3.4 24.5 - - - +
91L TYR* 3.7 33.9 - - + +
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Residues in contact with GLN 43 (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* 2.8 43.0 + - - +
95H PHE* 3.8 11.1 - - - -
42L LEU* 1.3 75.4 - - - +
44L LYS* 1.3 64.6 + - - +
45L PRO* 4.2 0.9 - - - +
47L GLN 3.3 26.1 - - - +
48L SER 4.5 0.7 - - - -
49L PRO* 3.8 25.6 - - + +
89L GLY* 3.8 0.5 - - - -
90L VAL* 2.8 43.6 + - - +
92L PHE* 3.3 21.4 - - + -
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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