Contacts of the strand formed by residues 38 - 43 (chain I) in PDB entry 3MQT
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 TYR 38 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I LYS* 3.9 23.1 - - + -
31I VAL 3.0 12.3 - - - +
32I THR* 3.7 15.7 - - + +
36I GLY 4.0 11.0 - - - -
37I VAL* 1.3 76.6 - - - +
39I GLY* 1.3 59.2 + - - +
40I LEU* 3.9 37.7 - - + +
112I LEU* 3.9 7.2 - - - -
115I LYS* 2.8 48.7 + - - +
373I LEU* 5.5 2.3 - - - +
375I ILE* 4.0 14.3 - - + +
386I PHE* 3.8 23.9 - + - -
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Residues in contact with GLY 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I VAL 3.6 0.7 - - - +
30I LYS* 3.5 5.7 - - - -
31I VAL 2.9 31.0 + - - -
38I TYR* 1.3 75.0 - - - +
40I LEU* 1.3 64.6 + - - +
108I ALA* 3.5 22.4 - - - +
111I ASP* 3.1 10.1 - - - -
112I LEU* 3.6 11.8 - - - +
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Residues in contact with LEU 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ILE* 3.9 24.0 - - + -
29I VAL 3.3 3.8 - - - +
30I LYS* 4.3 5.6 - - + -
38I TYR* 3.9 29.2 - - + -
39I GLY* 1.3 80.4 - - - +
41I GLY* 1.3 59.4 + - - +
108I ALA* 3.5 12.0 - - - -
111I ASP* 2.8 14.5 + - - +
115I LYS* 5.6 1.1 - - - +
315I ILE* 4.4 7.6 - - + -
369I LEU* 3.6 22.2 - - - +
371I ILE* 3.9 37.2 - - + +
373I LEU* 4.1 22.9 - - + -
386I PHE* 4.2 13.9 - - + -
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Residues in contact with GLY 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ILE* 3.6 5.9 - - - +
29I VAL 2.7 31.4 + - - -
40I LEU* 1.3 75.2 - - - +
42I GLU* 1.3 62.5 + - - +
104I GLY 3.6 17.5 - - - -
107I MET* 3.8 10.8 - - - -
108I ALA* 3.5 1.8 - - - +
315I ILE* 3.7 13.8 - - - +
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Residues in contact with GLU 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I THR* 2.5 29.0 + - - +
27I VAL 3.0 17.0 - - - +
29I VAL 4.5 0.4 - - - +
41I GLY* 1.3 76.3 - - - +
43I ALA* 1.3 58.7 + - - +
104I GLY* 3.3 14.8 + - - -
107I MET* 3.7 8.3 - - - +
284I ASN* 3.3 21.8 - - + +
312I LYS* 3.3 7.3 - - + +
313I THR* 3.0 40.0 + - - +
315I ILE* 3.7 14.4 - - + +
316I THR* 2.6 43.0 + - - +
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Residues in contact with ALA 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I PHE* 4.5 5.4 - - + -
26I THR* 4.3 1.7 + - - -
27I VAL* 3.1 37.5 + - + +
29I VAL* 4.3 8.5 - - + +
42I GLU* 1.3 76.0 - - - +
44I ASP* 1.3 68.2 + - - +
45I GLY 4.7 0.2 - - - +
50I MET* 4.9 2.7 - - + -
100I PHE 3.5 24.7 - - - +
101I ALA* 4.5 6.5 - - - -
104I GLY* 4.2 7.2 - - - -
284I ASN* 4.1 3.6 - - - -
312I LYS* 4.0 7.1 + - - -
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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