Contacts of the strand formed by residues 100 - 107 (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 ALA 100 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F GLN* 3.8 19.3 - - + +
44F GLN 3.3 15.5 - - - +
45F SER* 4.2 9.0 - - - +
97F GLY 5.4 0.9 - - - +
98F ASP 3.0 7.9 + - - +
99F SER* 1.3 75.3 - - - +
101F LEU* 1.3 61.8 + - - +
102F TYR* 3.4 22.7 - - + -
123F ARG* 4.3 0.8 - - - -
124F LEU 3.0 29.4 + - - +
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Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E GLN* 5.3 0.2 - - - +
47E SER 5.3 5.2 - - - +
48E GLN 5.8 0.4 - - - +
43F GLN* 3.6 1.2 - - - -
44F GLN* 2.7 56.9 + - + +
100F ALA* 1.3 72.1 - - - +
102F TYR* 1.3 60.9 + - - +
103F PHE* 3.6 34.6 + - + -
120F PRO 5.7 1.1 - - - +
121F GLY 5.0 2.5 - - - +
122F THR 3.4 19.3 - - - +
123F ARG* 3.4 55.4 - - + +
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Residues in contact with TYR 102 (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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6F GLN* 2.7 27.0 + - - -
21F LEU* 3.5 30.5 - - + -
41F TRP* 5.1 2.5 - - + -
42F TYR 3.5 11.7 - - - +
43F GLN* 2.9 40.0 + - + -
53F LEU* 4.5 2.2 - - + -
76F PHE* 4.2 12.0 - + - -
89F LEU* 4.4 10.3 - - + -
91F LEU* 4.0 22.8 - - + +
98F ASP* 2.9 28.5 + - - +
100F ALA* 3.4 23.8 - - + -
101F LEU* 1.3 72.2 - - - +
103F PHE* 1.3 57.6 + - - +
121F GLY* 3.1 0.3 - - - -
122F THR 2.7 29.3 + - - +
124F LEU* 3.9 18.6 - - + -
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Residues in contact with PHE 103 (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* 3.8 15.0 - - - -
47E SER 5.3 1.3 - - - -
48E GLN 4.2 3.8 - - - -
49E GLY* 3.5 22.7 - - - -
50E PRO* 4.3 6.3 - - + -
6F GLN* 4.0 0.7 - - - +
40F TYR 3.8 0.2 - - - +
41F TRP* 3.6 7.5 - - - -
42F TYR* 2.7 52.2 + - + +
44F GLN* 3.5 22.0 - - + -
50F LEU* 4.0 17.3 - - + -
101F LEU* 3.6 37.9 - - + -
102F TYR* 1.3 75.4 - - - +
104F CYS* 1.3 58.9 + - - +
118F PHE* 4.2 13.0 - + + -
119F GLY 3.6 11.9 - - - -
120F PRO 3.3 21.8 - - - -
121F GLY* 3.6 11.9 - - - -
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Residues in contact with CYS 104 (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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4F VAL* 4.2 2.2 - - + +
6F GLN* 3.1 21.9 + - - +
23F CYS* 2.0 53.8 - - + -
39F VAL* 4.6 7.9 - - - -
40F TYR 3.4 7.4 - - - -
41F TRP* 3.8 14.8 - - + -
87F SER* 5.8 0.2 - - - -
103F PHE* 1.3 74.0 - - - +
105F ALA* 1.3 71.4 + - - +
118F PHE* 3.5 4.4 - - - -
119F GLY 2.8 32.2 + - - -
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Residues in contact with ALA 105 (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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4F VAL* 4.9 0.7 - - - -
39F VAL* 3.2 10.2 - - - +
40F TYR* 2.7 54.0 + - + +
42F TYR* 4.3 0.9 - - + -
104F CYS* 1.3 80.1 - - - +
106F SER* 1.3 61.2 + - - +
116F GLN* 4.6 3.8 - - + +
117F TYR 3.4 8.5 - - - +
118F PHE* 3.7 32.5 - - + -
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Residues in contact with SER 106 (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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4F VAL* 3.5 26.2 - - - -
25F PRO* 3.3 14.6 - - - +
26F ARG* 3.2 9.5 + - - -
29F ASP* 2.7 37.3 + - - +
38F SER 3.2 5.3 + - - -
40F TYR* 4.3 2.0 - - - -
105F ALA* 1.3 77.0 - - - +
107F SER* 1.3 60.8 + - - +
116F GLN* 3.6 3.3 - - - -
117F TYR* 2.7 35.4 + - - -
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Residues in contact with SER 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F ASP* 3.1 7.4 - - - +
37F LEU 3.0 6.2 + - - -
38F SER* 3.0 31.4 + - - -
40F TYR* 3.4 28.3 - - - -
106F SER* 1.3 75.6 + - - +
108F VAL* 1.3 62.5 + - - +
109F ALA 2.7 23.9 + - - -
111F SER 3.4 12.6 + - - -
112F ALA* 5.4 0.4 - - - -
114F TYR* 4.5 3.6 - - - +
115F GLU 4.3 14.4 + - - -
116F GLN* 4.9 2.0 - - - -
117F TYR* 4.9 0.4 - - - -
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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