Contacts of the strand formed by residues 41 - 47 (chain L) in PDB entry 3IT8
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 HIS 41 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35L TYR* 3.5 11.5 - - - -
36L ASN* 2.9 22.3 + - - +
39L THR* 3.1 33.9 + - + +
40L ARG* 1.3 79.8 - - - +
42L GLY* 1.3 72.8 + - - +
43L ASN* 3.3 17.2 + - - -
67L ASN* 3.6 22.4 + - - +
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Residues in contact with GLY 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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33L ILE* 4.2 3.1 - - - -
34L SER 3.3 10.8 - - - -
41L HIS* 1.3 84.0 + - - +
43L ASN* 1.3 67.7 + - - +
63L ASP* 5.1 9.1 - - - +
66L PHE* 3.7 24.0 - - - -
67L ASN* 3.0 15.5 + - - +
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Residues in contact with ASN 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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33L ILE* 3.3 6.9 - - - +
34L SER* 3.0 30.3 + - - +
36L ASN* 2.9 45.4 - - - +
39L THR* 5.2 0.2 + - - -
41L HIS* 3.3 14.4 + - - -
42L GLY* 1.3 80.7 - - - +
44L VAL* 1.3 65.1 + - - +
45L ASN* 3.3 13.3 + - - +
63L ASP* 6.4 0.4 - - - -
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Residues in contact with VAL 44 (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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31L THR* 4.4 6.1 - - + -
32L LYS 3.5 6.5 - - - +
33L ILE* 3.9 15.7 - - + -
43L ASN* 1.3 73.8 - - - +
45L ASN* 1.3 60.2 + - - +
46L PHE 3.4 28.9 - - - +
47L ARG* 4.5 23.6 - - + +
63L ASP* 3.6 26.0 - - - +
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Residues in contact with ASN 45 (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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32L LYS* 2.8 39.6 + - + +
33L ILE 3.8 0.2 - - - -
34L SER* 2.5 43.6 + - - +
43L ASN* 3.4 14.1 - - - +
44L VAL* 1.3 76.9 - - - +
46L PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 46 (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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29L LEU* 3.6 48.9 - - + -
30L VAL 4.0 2.9 - - - -
31L THR* 3.3 4.9 - - - -
32L LYS* 3.1 37.6 + - + -
44L VAL* 3.4 11.6 - - - +
45L ASN* 1.3 83.7 - - + +
47L ARG* 1.3 78.0 + - - +
48L ALA* 3.4 28.0 - - + -
49L ASP* 5.6 1.3 - - - -
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Residues in contact with ARG 47 (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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30L VAL 3.3 5.6 - - - -
31L THR* 2.3 53.1 + - - +
44L VAL* 4.5 22.4 - - + +
46L PHE* 1.3 85.9 - - - +
48L ALA* 1.3 72.7 + - - +
49L ASP* 3.3 3.3 + - - -
51L PHE* 4.3 21.7 + - - +
53L ILE* 3.3 38.6 - - - +
63L ASP* 4.9 5.3 + - - -
64L TYR* 3.5 12.7 + - - -
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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