Contacts of the strand formed by residues 120 - 131 (chain C) in PDB entry 5FLX
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 GLN 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101 G 4.4 13.3 + - - +
113C GLN* 3.3 34.3 + - + +
114C LYS 3.3 9.6 - - - +
115C GLN* 4.2 15.8 + - - +
119C GLY* 1.3 74.6 - - - +
121C ARG* 1.3 61.4 + - - +
122C THR* 5.1 0.7 - - - +
349z C 5.3 9.9 + - - -
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Residues in contact with ARG 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13471 U 5.3 5.7 + - - -
13481 G 3.4 28.7 + - - +
14851 U 5.2 3.6 + - - -
14861 A 4.3 28.1 + - - -
113C GLN* 3.1 7.0 + - - +
114C LYS* 2.2 55.1 + - + +
116C THR* 4.6 6.0 + - - +
119C GLY 4.2 1.0 - - - -
120C GLN* 1.3 75.8 - - - +
122C THR* 1.3 77.6 + - - +
145C LYS* 6.1 2.5 - - - -
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C PRO* 4.3 3.6 - - - +
112C VAL 3.7 0.4 - - - -
113C GLN* 2.8 33.5 + - - +
114C LYS* 5.6 0.7 - - - -
120C GLN 5.1 0.7 - - - +
121C ARG* 1.3 91.3 - - - +
123C ARG* 1.3 75.7 + - - +
124C PHE* 4.1 19.8 - - + -
145C LYS* 4.0 14.7 - - - +
349z C 4.8 20.6 - - + +
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Residues in contact with ARG 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13481 G 4.0 26.6 + - - -
13491 G 3.7 23.7 + - - -
13571 A 5.6 2.0 - - - -
13581 U 6.0 5.7 - - - -
13591 U 5.1 8.2 + - - -
13611 G 6.1 1.2 - - - +
111C PRO* 3.5 3.3 - - - +
112C VAL* 2.6 63.4 + - + +
113C GLN 4.5 7.3 + - - +
114C LYS* 5.0 12.9 - - - +
122C THR* 1.3 77.2 + - - +
124C PHE* 1.3 63.0 + - - +
142C LYS* 5.4 4.0 - - - +
143C CYS* 3.8 42.8 + - + -
144C SER 3.3 15.3 - - - +
145C LYS* 3.7 8.7 - - + +
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Residues in contact with PHE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ILE* 4.0 17.9 - - + -
110C MET 3.8 2.0 - - - -
111C PRO* 4.0 23.3 - - + -
122C THR* 4.1 18.2 - - + -
123C ARG* 1.3 76.5 - - - +
125C LYS* 1.3 59.5 + - - +
126C ALA 4.1 0.2 - - - -
143C CYS* 3.2 2.4 - - - -
144C SER 2.4 53.4 + - - +
145C LYS 4.0 17.0 - - - -
146C GLU 4.8 3.8 - - - +
147C VAL* 3.5 35.2 - - + -
150C ALA* 3.9 9.0 - - + +
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Residues in contact with LYS 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13551 C 5.8 0.4 - - - -
13561 G 3.9 41.7 + - - -
108C LYS 3.9 0.7 - - - +
109C ILE* 3.2 3.4 - - - -
110C MET* 2.7 65.9 + - + +
112C VAL* 4.2 15.5 - - + -
123C ARG 4.2 0.2 + - - -
124C PHE* 1.3 73.3 - - - +
126C ALA* 1.3 60.0 + - - +
127C PHE* 3.6 29.1 - - + -
141C VAL* 3.3 22.4 - - + +
142C LYS 3.8 6.9 - - - +
143C CYS* 4.0 19.7 - - + +
234C GLY* 5.9 1.1 - - - -
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL* 5.0 0.7 - - + -
108C LYS 3.6 3.8 - - - -
109C ILE* 3.7 23.8 - - + -
124C PHE 4.1 0.6 + - - -
125C LYS* 1.3 73.8 - - - +
127C PHE* 1.3 74.1 + - - +
128C VAL* 4.2 5.4 - - + -
141C VAL* 4.0 1.9 - - - -
142C LYS 3.2 26.2 + - - +
150C ALA* 4.2 28.9 - - + +
151C ILE* 4.7 3.4 - - + +
154C ALA* 4.2 7.7 - - + +
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Residues in contact with PHE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL* 3.3 8.0 - - - +
107C LEU* 2.9 53.5 + - + -
108C LYS* 3.1 11.6 + - + +
110C MET* 3.6 22.7 - - + -
125C LYS* 3.6 25.6 - - + -
126C ALA* 1.3 79.7 - - - +
128C VAL* 1.3 61.6 + - - +
129C ALA 4.4 0.2 - - - -
139C LEU* 6.2 3.8 - - + -
140C GLY 4.2 3.6 - - - +
141C VAL* 3.4 32.3 - - + -
233C LEU* 3.5 27.8 - - + -
234C GLY* 3.5 37.9 - - - -
237C ALA* 5.6 2.2 - - + -
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ASP* 4.1 15.3 - - + +
105C GLU 4.6 4.9 - - - +
106C VAL* 4.2 18.4 - - + -
107C LEU* 5.5 0.7 - - - -
126C ALA* 4.2 2.6 - - + -
127C PHE* 1.3 80.8 - - - +
129C ALA* 1.3 64.0 + - - +
130C ILE* 4.2 9.6 - - + -
139C LEU* 3.9 2.2 - - - +
140C GLY* 3.2 31.4 + - - +
151C ILE* 4.5 17.3 - - + +
154C ALA* 3.7 25.7 - - + +
155C ILE* 3.7 25.8 - - + -
158C ALA* 3.9 4.3 - - - +
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ASP* 3.3 19.8 - - - +
105C GLU 3.9 12.1 + - - +
107C LEU* 4.9 11.6 - - + +
128C VAL* 1.3 75.1 - - - +
130C ILE* 1.3 63.1 + - - +
138C GLY 3.4 11.9 - - - +
139C LEU* 4.1 21.1 - - + -
213C LEU* 4.2 17.7 - - + -
216C MET* 4.1 14.6 - - + +
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Residues in contact with ILE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ILE* 4.4 7.4 - - + -
101C SER* 4.1 12.8 - - - +
102C LEU* 5.4 0.9 - - - +
103C LYS 4.0 4.7 - - - -
104C ASP* 3.5 26.5 - - + +
128C VAL* 4.2 5.6 - - + -
129C ALA* 1.3 78.8 - - - +
131C GLY* 1.3 59.7 + - - +
137C VAL* 3.3 5.7 - - - +
138C GLY 2.8 32.4 + - - +
155C ILE* 5.1 7.4 - - + -
158C ALA* 3.3 45.8 - - + +
159C LYS* 3.5 33.7 - - + +
162C ILE* 5.4 4.3 - - + -
213C LEU* 5.7 0.3 - - - +
216C MET* 5.0 5.1 - - - +
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Residues in contact with GLY 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C SER* 3.8 16.4 + - - +
103C LYS* 3.3 24.4 + - - +
130C ILE* 1.3 80.9 - - - +
132C ASP* 1.3 62.6 + - - -
133C TYR* 5.5 1.9 - - - -
136C HIS 3.1 13.9 - - - -
137C VAL* 3.7 8.5 - - - -
162C ILE* 5.1 2.0 - - - -
216C MET* 4.6 8.5 - - - +
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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