Contacts of the strand formed by residues 99 - 109 (chain H) in PDB entry 3F5O
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 ASP 99 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41H GLU* 4.8 7.0 - - + +
42H MET 3.5 4.2 - - - -
43H LYS* 3.3 34.7 + - - +
97H GLY 3.9 1.6 + - - +
98H GLU* 1.3 73.4 - - - +
100H ILE* 1.3 63.6 + - - +
122H ASN* 3.8 6.8 - - - +
123H LYS* 2.9 52.1 + - + +
124H ALA 4.6 0.3 + - - -
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Residues in contact with ILE 100 (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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41H GLU* 3.2 7.7 - - - +
42H MET* 2.8 60.9 + - + +
44H VAL* 3.9 19.3 - - + -
55H LEU* 3.9 24.7 - - + -
63H LEU* 4.1 6.1 - - + -
94H ALA* 4.0 5.2 - - + -
98H GLU* 4.4 4.3 - - + +
99H ASP* 1.3 80.7 - - - +
101H VAL* 1.3 63.2 + - - +
102H ILE* 4.0 11.4 - - + -
120H LEU* 4.0 17.7 - - + -
121H THR 3.3 8.3 - - - +
122H ASN* 5.0 0.2 - - - -
123H LYS* 4.7 0.2 - - - -
129H ILE* 3.4 25.8 - - + -
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Residues in contact with VAL 101 (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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39H ILE* 3.7 22.7 - - + -
40H CYS 3.4 10.1 - - - +
41H GLU* 3.8 15.0 - - + +
100H ILE* 1.3 76.8 - - - +
102H ILE* 1.3 64.2 + - - +
103H THR* 3.7 12.6 - - - +
119H ASP 3.6 1.4 - - - +
120H LEU* 3.2 6.4 - - - +
121H THR* 2.8 45.5 + - - +
123H LYS* 3.7 35.2 - - + +
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Residues in contact with ILE 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ILE* 5.2 0.9 - - + -
38H VAL 3.7 1.9 - - - +
39H ILE* 3.4 2.4 - - - -
40H CYS* 2.8 59.4 + - + +
41H GLU 4.1 8.3 - - - +
42H MET* 4.3 2.7 - - + -
63H LEU* 4.2 25.4 - - + +
67H ILE* 4.0 23.5 - - + +
100H ILE* 4.0 24.0 - - + +
101H VAL* 1.3 77.2 - - - +
103H THR* 1.3 59.2 + - - +
104H ALA 4.1 0.2 + - - -
118H VAL* 3.6 27.4 - - + -
119H ASP 3.6 1.8 - - - -
120H LEU* 4.0 25.1 - - + +
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Residues in contact with THR 103 (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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37H LYS* 4.0 28.0 - - - +
38H VAL 3.5 3.1 - - - +
39H ILE* 4.0 14.6 - - + +
101H VAL* 3.7 18.2 - - - +
102H ILE* 1.3 73.7 + - - +
104H ALA* 1.3 63.6 + - - +
105H HIS* 4.3 7.2 + - + +
117H SER 3.9 0.7 - - - +
118H VAL* 3.3 4.6 - - - -
119H ASP* 2.9 47.7 + - + +
121H THR* 5.3 1.6 + - - -
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Residues in contact with ALA 104 (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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37H LYS* 3.3 7.6 - - - +
38H VAL* 2.8 32.9 + - + +
67H ILE* 3.5 42.0 - - + +
68H SER* 3.8 6.1 - - - -
71H ALA* 4.1 5.5 - - + +
102H ILE 4.1 0.6 + - - -
103H THR* 1.3 75.2 - - - +
105H HIS* 1.3 61.2 + - - +
117H SER 3.4 4.9 - - - -
118H VAL* 3.8 14.1 - - + -
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Residues in contact with HIS 105 (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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131E GLN* 5.6 1.1 + - - -
36H GLY 3.2 10.3 - - - +
37H LYS* 4.6 10.8 - - + -
71H ALA* 4.8 2.0 - - - -
103H THR* 5.0 7.4 + - + +
104H ALA* 1.3 77.9 - - - +
106H VAL* 1.3 70.8 + - - +
107H LEU* 3.2 25.1 + - + +
116H THR* 3.3 5.0 + - - -
117H SER* 2.5 63.3 + - - -
119H ASP* 5.8 6.1 - - - -
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Residues in contact with VAL 106 (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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36H GLY* 2.9 25.2 + - - +
71H ALA* 3.6 33.4 - - + +
72H LEU* 3.6 29.6 - - + +
75H THR* 4.3 1.8 - - + -
105H HIS* 1.3 79.0 - - - +
107H LEU* 1.3 63.3 + - - +
108H LYS 4.1 15.3 - - - +
109H GLN* 4.1 22.4 - - + +
115H PHE 3.7 9.6 - - - +
116H THR* 4.1 3.8 - - - +
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Residues in contact with LEU 107 (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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91E MET* 3.8 26.0 - - + -
128E LEU* 4.0 24.5 - - + +
131E GLN* 3.8 29.6 - - - +
105H HIS* 3.2 35.4 - - + +
106H VAL* 1.3 74.8 - - - +
108H LYS* 1.3 60.1 + - - +
115H PHE* 2.7 16.2 + - + +
116H THR 4.2 6.7 - - - +
117H SER* 3.3 20.4 - - - +
133H ARG* 4.2 11.7 - - + -
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Residues in contact with LYS 108 (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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91E MET* 3.3 45.1 - - + +
92E SER* 4.8 9.0 - - - -
127E LYS* 5.9 7.6 - - + -
128E LEU* 5.7 2.7 - - + +
150F COA 2.9 30.3 + - - -
106H VAL* 3.6 5.8 - - - +
107H LEU* 1.3 81.2 - - - +
109H GLN* 1.3 79.9 + - - +
110H GLY* 3.4 8.7 - - - +
114H ALA* 3.5 1.4 - - - -
115H PHE* 2.8 43.5 + - + +
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Residues in contact with GLN 109 (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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36H GLY* 5.9 1.0 - - - -
72H LEU* 5.3 2.7 - - + +
75H THR* 3.5 39.8 + - - +
76H GLU 5.2 0.4 + - - -
77H ARG* 4.8 10.1 + - - +
106H VAL* 4.1 15.5 - - + +
108H LYS* 1.3 88.5 + - - +
110H GLY* 1.3 63.2 + - - +
113H LEU 3.9 2.5 - - - -
114H ALA* 4.4 9.2 - - + +
138H LEU* 5.2 4.9 - - + -
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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