Contacts of the helix formed by residues 116 - 129 (chain A) in PDB entry 6FP4
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLY 3.4 6.1 + - - -
115A GLY* 1.3 77.0 - - - +
117A SER* 1.3 67.6 + - - +
118A GLY 3.4 2.2 - - - -
119A GLY 4.0 1.8 - - - +
120A LEU* 2.9 25.7 + - - +
151A GLY 3.4 15.0 - - - -
152A GLY* 3.4 4.3 - - - -
601A FAD 3.2 23.4 + - - -
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLY* 1.3 72.1 - - - +
118A GLY* 1.3 63.7 + - - +
120A LEU* 4.4 1.3 - - - +
121A ALA* 3.2 22.0 + - - +
151A GLY 3.8 5.8 + - - -
154A CYS* 3.7 8.5 - - - +
155A VAL* 5.7 1.0 - - - +
442A THR* 3.1 48.7 + - - +
445A ALA* 4.2 0.9 - - - -
446A ILE* 3.7 10.2 - - - +
601A FAD 3.4 26.3 + - - -
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Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 1.3 77.0 - - - +
119A GLY* 1.3 60.1 + - - +
121A ALA* 3.1 2.1 + - - +
122A ALA* 2.8 33.1 + - - +
431A ILE* 3.4 15.9 - - - +
445A ALA* 3.4 31.5 - - - +
449A GLY* 4.3 0.3 - - - -
601A FAD 3.1 10.1 + - - -
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Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 3.3 24.8 - - - +
114A GLY 3.3 22.0 - - - -
115A GLY* 5.1 0.2 - - - -
116A GLY 3.5 3.4 + - - -
118A GLY* 1.3 75.5 - - - +
120A LEU* 1.3 57.2 + - - +
122A ALA* 3.6 0.6 + - - +
123A GLY* 2.9 26.0 + - - -
135A VAL* 4.5 2.6 - - - +
256A ALA* 3.7 14.6 - - - +
431A ILE* 4.3 1.6 - - - -
601A FAD 3.9 1.6 + - - -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLY 3.4 23.3 - - - +
116A GLY 2.9 17.5 + - - +
117A SER* 4.4 1.3 - - - +
119A GLY* 1.3 75.3 - - - +
121A ALA* 1.3 58.6 + - - +
123A GLY* 5.1 0.7 - - - -
124A LYS* 2.8 34.7 + - - +
135A VAL* 4.1 13.5 - - + -
150A LEU* 4.1 9.6 - - + -
151A GLY* 3.7 21.8 - - - +
212A TYR* 3.8 35.0 - - + -
216A LEU* 3.6 40.1 - - + +
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A SER 3.2 18.4 + - - +
118A GLY 3.1 3.7 + - - +
120A LEU* 1.3 78.9 - - - +
122A ALA* 1.3 62.3 + - - +
124A LYS* 3.9 4.1 - - - +
125A GLU* 3.0 25.8 + - - +
446A ILE* 3.8 26.5 - - + +
450A ARG* 3.7 32.2 - - + +
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.6 1.8 - - - -
112A VAL* 4.8 1.3 - - + -
118A GLY 2.8 19.4 + - - +
119A GLY* 3.9 2.7 - - - +
121A ALA* 1.3 73.9 - - - +
123A GLY* 1.3 57.7 + - - +
125A GLU 3.3 0.2 + - - -
126A ALA* 2.9 31.1 + - - +
254A ILE* 3.8 26.5 - - + -
431A ILE* 3.8 6.3 - - + -
449A GLY* 3.5 31.8 - - - +
453A ALA* 3.4 4.9 - - + +
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Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.3 1.6 - - - -
112A VAL* 4.1 8.9 - - - +
119A GLY 2.9 18.7 + - - -
120A LEU 3.8 0.4 - - - -
122A ALA* 1.3 77.1 - - - +
124A LYS* 1.3 62.0 + - - +
126A ALA* 3.4 1.7 + - - +
127A ALA* 3.2 23.4 + - - +
133A THR* 3.9 23.8 - - - +
135A VAL* 4.4 7.6 - - - -
216A LEU* 5.4 0.2 - - - -
221A VAL* 4.0 5.6 - - - +
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU 2.8 18.4 + - - +
121A ALA* 3.9 5.2 - - - +
123A GLY* 1.3 77.3 - - - +
125A GLU* 1.3 61.1 + - - +
127A ALA* 3.5 3.1 + - - +
128A LYS* 3.4 18.7 + - - +
212A TYR* 6.5 0.7 - - + -
215A ALA* 4.7 22.0 - - + +
216A LEU* 5.0 9.4 - - + +
219A ASN* 3.5 31.3 + - + +
221A VAL* 4.9 6.5 - - - -
450A ARG* 5.5 9.1 - - - +
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ALA 3.0 19.0 + - - +
124A LYS* 1.3 75.0 - - - +
126A ALA* 1.3 63.5 + - - +
128A LYS* 3.0 36.4 + - - +
129A TYR* 3.3 31.4 + - + -
450A ARG* 3.5 40.1 - - + +
453A ALA* 3.7 12.3 - - + -
454A ARG* 2.6 36.8 + - + -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 3.4 26.5 - - + -
122A ALA 2.9 17.9 + - - +
123A GLY 3.7 3.8 - - - +
124A LYS 3.2 0.2 - - - -
125A GLU* 1.3 78.6 - - - +
127A ALA* 1.3 63.1 + - - +
129A TYR* 2.9 18.0 + - - +
131A ALA* 3.3 28.4 + - + +
133A THR* 3.9 1.3 - - - +
453A ALA* 3.7 8.7 - - + +
457A PHE* 3.8 13.8 - - + +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LYS* 3.4 22.3 - - - +
123A GLY 3.2 6.0 + - - +
124A LYS 4.0 3.6 - - - +
125A GLU 3.4 0.2 - - - -
126A ALA* 1.3 77.9 - - - +
128A LYS* 1.3 63.6 + - - +
129A TYR 3.1 0.9 + - - -
130A GLY* 3.2 9.2 + - - -
131A ALA 3.5 19.7 - - - +
133A THR* 3.9 2.3 + - - +
219A ASN* 3.3 29.8 - - + +
220A GLN 5.2 1.3 - - - +
221A VAL* 3.5 20.2 - - + -
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Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LYS* 4.0 15.2 - - - +
45A HIS 4.3 4.5 + - - +
124A LYS 3.4 7.5 + - - +
125A GLU* 3.0 38.9 + - - +
126A ALA 3.0 0.4 - - - -
127A ALA* 1.3 78.7 - - - +
129A TYR* 1.3 85.5 + - + +
130A GLY 3.9 0.3 + - - -
219A ASN* 5.5 4.4 - - - +
454A ARG* 6.2 0.2 - - - +
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Residues in contact with TYR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 4.5 0.2 - - - +
20A VAL 3.5 19.2 + - - +
45A HIS* 4.0 13.2 - - - -
46A ALA* 3.7 20.8 + - - +
47A THR 5.7 0.9 - - - -
125A GLU* 3.3 50.3 + - + -
126A ALA* 2.9 7.6 + - - +
128A LYS* 1.3 102.8 - - + +
130A GLY* 1.3 58.0 + - - +
131A ALA 3.4 3.5 + - - -
453A ALA 4.8 4.0 - - - -
454A ARG* 3.8 24.3 + - + +
457A PHE* 3.5 26.0 - - + +
458A ALA* 3.8 20.9 - - + -
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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