Contacts of the strand formed by residues 49 - 57 (chain F) in PDB entry 4GG6
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 GLY 49 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103E TYR* 5.8 1.3 - - - -
119E GLY 3.7 12.3 - - - -
120E LYS* 5.2 4.3 - - - -
43F GLN 3.5 1.0 - - - +
44F GLN* 3.1 12.8 - - - -
45F SER* 3.0 32.1 + - - -
46F LEU 4.6 1.6 + - - -
47F ASP 3.7 1.8 - - - -
48F GLN* 1.3 79.8 - - - +
50F LEU* 1.3 59.0 + - - -
51F GLN 3.5 2.9 + - - -
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Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E GLN* 4.0 4.9 - - - +
50E PRO* 3.6 31.0 - - + -
103E TYR* 4.2 8.0 + - + +
118E PHE* 2.8 73.7 + - + +
119E GLY 3.6 2.4 + - - -
42F TYR* 3.9 21.4 - - + -
44F GLN* 3.5 41.9 - - + +
48F GLN 4.9 0.2 - - - -
49F GLY* 1.3 68.3 - - - -
51F GLN* 1.3 59.6 + - - +
52F PHE 3.9 0.2 + - - -
103F PHE* 4.0 18.2 - - + -
118F PHE* 5.0 0.2 - - + -
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Residues in contact with GLN 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E THR* 3.0 29.7 + - - +
118E PHE 5.3 0.3 - - - +
42F TYR* 3.2 6.7 - - - -
43F GLN* 2.7 54.6 + - + +
48F GLN* 3.6 42.3 + - + +
49F GLY 3.5 2.2 + - - +
50F LEU* 1.3 73.0 - - - +
52F PHE* 1.3 63.3 + - - +
53F LEU* 5.2 4.0 - - + -
70F ASN* 3.0 33.0 + - + +
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Residues in contact with PHE 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ALA* 4.6 8.5 - - - -
116E LEU* 3.5 37.2 - - + -
117E THR* 3.5 35.7 - - + +
40F TYR* 3.9 8.3 - + + -
41F TRP 3.7 5.8 - - - -
42F TYR* 3.7 21.2 - + + -
51F GLN* 1.3 74.6 + - - +
53F LEU* 1.3 71.6 + - - +
54F ILE 3.4 19.3 - - - -
55F GLN* 3.4 29.8 - - + -
67F ALA* 3.4 18.4 - - + -
68F LYS 4.1 2.5 - - - -
69F GLY* 3.9 12.8 - - - -
70F ASN* 3.8 21.7 + - - +
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F TRP* 2.8 21.0 + - + +
42F TYR 3.8 21.3 - - - +
43F GLN* 4.0 28.5 - - + +
51F GLN* 5.1 4.3 - - + +
52F PHE* 1.3 78.5 - - - +
54F ILE* 1.3 62.2 + - + +
68F LYS* 3.7 0.5 - - - -
69F GLY* 2.7 31.8 + - - -
70F ASN 4.5 6.7 - - - +
71F ILE* 3.7 36.4 - - + +
76F PHE* 4.6 17.0 - - + -
89F LEU* 4.1 25.1 - - + -
102F TYR* 4.5 5.6 - - + -
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Residues in contact with ILE 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F VAL 4.1 0.9 - - - +
40F TYR* 3.6 0.3 - - - -
41F TRP* 2.8 49.3 + - + -
52F PHE* 3.4 6.2 - - - -
53F LEU* 1.3 85.5 - - + +
55F GLN* 1.3 63.2 + - - +
56F TYR* 3.3 40.4 - - + +
65F GLU* 3.7 23.3 - - + +
67F ALA 3.2 11.4 - - - +
68F LYS* 5.0 0.2 - - + -
71F ILE* 3.9 30.1 - - + -
78F ALA* 4.0 16.6 - - + +
89F LEU* 5.2 3.4 - - + -
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Residues in contact with GLN 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E GLY* 5.8 2.4 + - - -
116E LEU* 4.2 4.7 - - - +
38F SER* 3.3 18.2 + - - -
39F VAL 3.3 11.9 - - - +
40F TYR* 3.4 28.6 + - + -
52F PHE* 3.6 14.6 - - + -
54F ILE* 1.3 74.8 - - - +
56F TYR* 1.3 68.8 + - - +
57F TYR* 4.4 0.4 - - - +
65F GLU* 3.7 3.5 - - - +
66F ARG* 2.8 54.4 + - - +
67F ALA* 2.7 25.7 + - - +
110F VAL* 2.8 28.4 + - - +
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Residues in contact with TYR 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F SER* 3.3 6.1 - - - -
39F VAL* 2.8 49.7 + - + +
41F TRP* 4.8 2.5 - + - -
54F ILE* 3.3 38.4 - - + +
55F GLN* 1.3 77.9 - - - +
57F TYR* 1.3 60.0 + - - +
63F GLY 4.0 3.6 - - - -
64F GLU 3.7 4.9 - - - +
65F GLU* 3.5 35.3 + - + -
78F ALA* 2.6 44.9 + - + +
79F GLN* 3.6 15.7 - - + -
80F GLN* 3.6 34.4 - - + +
87F SER* 4.6 1.8 - - - -
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Residues in contact with TYR 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ALA* 3.6 43.8 - - + +
65C VAL* 4.2 12.2 - - - +
68C HIS* 4.0 14.6 - - - +
37F LEU* 3.7 39.6 - - + +
38F SER* 3.2 22.2 - - - +
55F GLN* 4.4 0.4 - - - +
56F TYR* 1.3 73.6 - - - +
58F ASN* 1.3 77.1 + - + +
63F GLY 3.2 1.8 - - - -
64F GLU* 3.0 24.4 + - - +
66F ARG* 3.8 15.7 + - + +
108F VAL 4.8 0.2 - - - -
109F ALA* 3.9 4.3 - - - +
110F VAL* 3.4 45.7 + - + -
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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