Contacts of the strand formed by residues 46 - 52 (chain H) in PDB entry 3QUM
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 GLU 46 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37H VAL* 3.3 5.6 - - - +
38H LYS* 2.7 59.2 + - + +
44H GLY 5.0 0.9 - - - +
45H LEU* 1.3 77.0 - - - +
47H TRP* 1.3 63.8 + - - +
48H ILE 3.8 0.3 + - - -
60H ASN* 5.3 2.7 - - - +
62H LYS* 2.7 44.7 + - + +
63H PHE* 3.7 24.9 - - + -
98L PHE* 4.6 4.0 - - - +
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Residues in contact with TRP 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ASN* 3.4 25.4 - - + +
36H TRP 4.0 9.2 - - - -
37H VAL* 4.6 2.9 - - + -
46H GLU* 1.3 76.2 - - - +
48H ILE* 1.3 61.2 + - - +
49H GLY* 3.5 24.8 + - - -
50H ARG* 3.8 18.4 - - + -
58H LYS 3.6 18.2 - - - -
59H TYR 4.4 2.5 - - - -
60H ASN* 3.2 44.9 + - + +
63H PHE* 4.1 3.5 - - - -
100H PHE* 3.8 16.2 + - - -
94L TYR* 3.7 25.4 - + - -
95L PRO* 4.1 12.8 - - + -
96L VAL* 3.5 62.1 + - + +
98L PHE* 4.4 6.4 - + + -
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Residues in contact with ILE 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H TRP* 3.1 24.0 + - + +
37H VAL* 4.4 3.4 - - - -
38H LYS* 4.3 13.0 - - + -
47H TRP* 1.3 74.6 - - - +
49H GLY* 1.3 59.2 + - - +
59H TYR* 3.8 9.1 - - + +
60H ASN* 3.2 17.7 + - - +
63H PHE* 3.9 36.0 - - + +
67H ALA* 3.8 26.7 - - + -
69H LEU* 4.8 8.1 - - + -
80H MET* 3.7 28.7 - - + -
82H LEU* 5.0 2.0 - - + -
90H TYR* 4.1 22.9 - - + -
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Residues in contact with GLY 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ASN* 3.6 2.4 - - - +
36H TRP* 3.4 23.5 + - - -
47H TRP* 3.5 20.5 - - - -
48H ILE* 1.3 78.7 - - - +
50H ARG* 1.3 62.3 + - - +
58H LYS 3.4 13.7 - - - -
59H TYR* 4.0 3.8 - - - -
69H LEU* 3.6 14.3 - - - +
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Residues in contact with ARG 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H TRP* 3.1 62.3 - - + +
34H MET 3.6 8.5 - - - +
35H ASN* 3.5 23.7 - - - +
47H TRP* 4.0 11.2 - - + -
49H GLY* 1.3 74.6 - - - -
51H ILE* 1.3 61.8 + - - +
57H THR* 3.3 4.7 - - - -
58H LYS* 3.2 37.4 + - + +
69H LEU* 3.7 7.3 - - - +
95H ASP* 2.5 31.3 + - - -
100H TYR* 4.3 15.6 - - - -
91L HIS* 4.8 4.3 - - - -
94L TYR* 2.8 33.0 + - - -
24P LYS 6.0 0.4 + - - -
25P HIS* 5.4 2.8 + - - +
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Residues in contact with ILE 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H TRP* 3.5 4.7 - - - -
34H MET* 3.0 42.1 + - + +
36H TRP* 4.9 6.1 - - - +
50H ARG* 1.3 76.8 - - - +
52H TYR* 1.3 82.0 + - + +
55H GLY* 4.1 13.0 - - - +
56H ASP 3.0 14.8 - - - +
57H THR* 4.0 8.7 - - + -
69H LEU* 4.1 21.1 - - + +
70H THR* 3.9 25.8 - - - +
71H VAL* 3.8 31.9 - - + +
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Residues in contact with TYR 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H SER 3.1 25.3 + - - -
31H SER* 3.5 22.2 + - - -
33H TRP* 3.4 40.1 - + + -
51H ILE* 1.3 71.0 - - - +
52H PRO* 1.3 63.2 + - + +
53H GLY* 3.1 28.5 + - - -
54H ASP* 3.3 9.2 - - - +
55H GLY* 3.1 20.1 + - - -
56H ASP 2.7 15.0 + - - +
28P PRO* 4.9 4.7 - - + -
29P TRP* 3.2 29.5 - + - -
119P LYS* 2.8 51.6 - - + -
120P VAL 4.3 10.0 + - - -
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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