Contacts of the helix formed by residues 122 - 142 (chain B) in PDB entry 2FGY
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 ASN 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLU 5.2 1.2 + - - -
112B LEU* 3.4 49.2 + - - +
114B LYS 4.9 6.9 + - - +
115B ASP* 4.6 3.8 + - - +
116B ASN* 6.1 1.1 - - - +
120B GLY 3.5 2.7 + - - +
121B HIS* 1.3 69.9 - - - +
123B LEU* 1.3 55.0 + - - +
124B LYS* 3.9 4.0 + - - +
125B GLY* 2.9 24.4 + - - -
126B ILE* 2.9 33.0 + - + +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.7 35.0 - - + +
83B VAL* 3.7 31.9 - - + -
84B ALA* 3.8 24.0 - - + +
121B HIS* 2.9 26.0 + - + +
122B ASN* 1.3 72.6 - - - +
124B LYS* 1.3 59.7 + - + +
126B ILE* 4.5 1.3 - - + -
127B PHE* 2.9 31.0 + - - +
449B PRO* 5.9 0.2 - - - -
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Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASN* 3.3 4.2 + - - +
123B LEU* 1.3 78.7 - - + +
125B GLY* 1.3 57.2 + - - +
127B PHE* 3.7 1.4 - - - +
128B GLY 3.2 21.5 + - - -
447B GLY 4.9 7.6 - - - +
449B PRO* 3.8 20.8 - - + +
490B GLN* 2.9 34.5 + - - +
491B ASN* 3.6 25.9 - - + +
492B LEU* 3.8 17.8 - - + +
494B GLN* 3.2 16.7 - - - +
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.6 15.6 - - - +
122B ASN* 2.9 25.6 + - - -
124B LYS* 1.3 75.1 - - - +
126B ILE* 1.3 59.3 + - - +
128B GLY* 3.6 1.0 + - - -
129B TYR* 3.0 29.3 + - - +
494B GLN* 4.1 11.0 - - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.8 21.3 - - + -
80B LEU* 3.6 17.3 - - + -
83B VAL* 4.4 22.0 - - + -
96B VAL* 5.0 1.6 - - + -
108B LEU* 4.4 16.2 - - + -
112B LEU* 4.1 28.7 - - + +
113B LEU* 3.9 25.1 - - + -
121B HIS* 5.5 0.4 - - + -
122B ASN 2.9 28.7 + - - +
123B LEU* 4.0 4.7 - - + +
125B GLY* 1.3 71.6 - - - +
127B PHE* 1.3 56.8 + - - +
129B TYR* 3.7 0.9 - - - +
130B ALA* 2.8 37.1 + - + +
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE 6.1 0.2 - - - -
76B VAL* 4.0 11.4 - - + -
77B ILE* 3.8 22.9 - - + -
80B LEU* 3.6 27.5 - - + +
123B LEU 2.9 20.2 + - - +
124B LYS 3.7 4.0 - - - +
126B ILE* 1.3 75.6 - - - +
128B GLY* 1.3 58.3 + - - +
130B ALA* 3.8 1.0 - - - +
131B THR* 2.8 51.9 + - + -
400B ARG 5.4 0.4 - - - -
443B ASN* 3.8 14.1 - - - -
448B LEU* 4.0 8.3 - - + -
449B PRO* 3.3 51.8 - - + -
451B PRO* 3.9 23.1 - - + -
494B GLN* 4.6 0.2 - - + -
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS 3.2 8.3 + - - -
125B GLY 3.9 0.2 - - - -
127B PHE* 1.3 80.0 - - - +
129B TYR* 1.3 61.3 + - - +
131B THR* 3.4 4.6 + - - -
132B ALA* 2.9 25.1 + - - +
451B PRO* 5.7 0.9 - - - -
494B GLN* 3.7 35.9 - - - -
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Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B HIS* 4.1 1.6 - + - -
107B THR* 3.8 18.6 + - - +
108B LEU* 3.7 17.5 - - + -
109B PRO* 3.5 29.2 - - + +
112B LEU* 3.4 29.4 - - + -
125B GLY 3.0 9.9 + - - +
126B ILE* 3.7 2.9 - - - +
128B GLY* 1.3 74.2 - - - +
130B ALA* 1.3 65.4 + - - +
132B ALA* 3.2 7.0 + - + +
133B LYS* 2.9 54.7 + - + +
494B GLN* 4.8 0.4 + - - -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 3.9 30.9 - - + +
79B PHE* 5.5 0.2 - - + -
104B LEU* 4.1 22.0 - - + -
106B HIS* 4.3 15.5 + - + -
108B LEU* 5.3 1.3 - - + -
126B ILE* 2.8 26.1 + - + +
129B TYR* 1.3 75.2 - - + +
131B THR* 1.3 56.9 + - - +
133B LYS* 3.5 2.3 + - - +
134B ALA* 2.9 28.2 + - - +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 3.6 30.2 + - + -
76B VAL* 4.2 8.8 - - - +
127B PHE* 2.8 41.7 + - + -
128B GLY* 3.8 5.6 - - - -
129B TYR 3.2 0.2 - - - -
130B ALA* 1.3 74.7 - - - +
132B ALA* 1.3 64.0 + - - +
134B ALA* 3.4 5.1 + - - -
135B LEU* 3.1 18.4 + - - +
400B ARG 4.9 2.0 - - - +
401B TYR* 5.1 2.5 - - + -
451B PRO* 3.7 32.1 - - + -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLY 2.9 17.5 + - - +
129B TYR* 3.2 8.3 + - + +
131B THR* 1.3 77.2 - - - +
133B LYS* 1.3 56.6 - - + +
135B LEU* 3.2 9.5 + - - +
136B THR* 3.0 30.7 + - - -
495B PHE 5.6 1.3 - - - +
496B ARG* 3.5 34.9 + - + +
510B GLU* 4.9 4.3 - - - +
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B HIS* 3.7 50.1 - - + +
107B THR 5.4 0.2 - - - -
129B TYR* 2.9 52.7 + - + +
130B ALA 3.7 0.7 - - - +
132B ALA* 1.3 74.0 - - + +
134B ALA* 1.3 59.4 + - - +
136B THR* 3.6 14.0 - - + +
137B ALA* 2.8 32.2 + - - +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG* 3.6 43.1 - - + +
73B PHE* 4.0 17.3 - - + +
76B VAL* 5.0 0.4 - - + -
106B HIS* 5.4 0.4 + - - -
130B ALA 2.9 17.7 + - - +
131B THR* 3.4 6.9 + - - +
133B LYS* 1.3 74.6 - - - +
135B LEU* 1.3 56.6 + - - +
137B ALA* 3.6 2.9 + - - -
138B ALA* 3.0 30.8 + - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PHE* 3.7 14.3 - - + -
131B THR 3.1 12.6 + - - +
132B ALA* 3.2 10.5 + - - +
134B ALA* 1.3 72.6 - - - +
136B THR* 1.3 65.7 + - - +
138B ALA* 3.3 1.5 + - + -
139B THR* 3.0 45.3 + - + +
401B TYR* 3.5 33.0 - - + +
408B PHE* 3.8 12.6 - - + -
411B VAL* 4.2 7.0 - - + -
453B ALA* 3.7 29.6 - - + -
496B ARG* 3.5 27.6 - - + +
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA 3.0 11.1 + - - -
133B LYS* 3.4 19.4 + - + +
135B LEU* 1.3 74.5 - - - +
137B ALA* 1.3 65.2 + - - +
139B THR* 3.2 5.7 + - - -
140B GLU* 2.9 49.7 + - + +
496B ARG* 3.0 13.4 + - - +
510B GLU* 2.6 30.0 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 3.5 37.3 + - - +
133B LYS 2.8 21.4 + - - +
134B ALA* 3.9 0.7 - - - +
136B THR* 1.3 75.0 - - - +
138B ALA* 1.3 58.0 + - - +
140B GLU* 4.0 6.1 - - - +
141B GLN* 3.0 32.2 + - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B VAL* 3.9 33.2 - - + -
72B ARG* 4.0 12.1 - - - +
73B PHE* 4.7 2.9 - - + -
134B ALA 3.0 19.7 + - - +
135B LEU* 3.9 4.9 - - - +
137B ALA* 1.3 75.7 - - - +
139B THR* 1.3 61.8 + - - +
141B GLN* 4.7 2.5 - - - -
142B PHE* 3.2 32.2 + - - +
411B VAL* 4.0 11.3 - - + +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 3.0 38.9 + - + +
136B THR* 3.2 11.1 + - - -
138B ALA* 1.3 74.2 - - - +
140B GLU* 1.3 66.6 + - - +
142B PHE 3.9 0.3 - - - -
143B SER* 3.1 25.3 + - - -
408B PHE* 4.2 5.4 - - + -
410B GLU* 3.9 20.7 - - + +
411B VAL* 4.1 17.0 - - + -
496B ARG* 4.9 2.9 + - - +
508B ILE* 3.7 34.2 - - + +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B THR* 2.9 42.8 + - + +
137B ALA* 4.0 5.3 - - - +
139B THR* 1.3 81.7 + - - +
141B GLN* 1.3 64.8 + - - +
142B PHE 3.3 0.5 + - - -
143B SER* 3.3 16.5 + - - -
508B ILE* 5.6 2.0 - - + +
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B SER* 3.8 11.5 + - - -
72B ARG* 2.9 31.7 + - - +
137B ALA 3.0 16.8 + - - +
138B ALA 4.0 0.4 - - - +
140B GLU* 1.3 78.8 - - - +
142B PHE* 1.3 93.5 + - + +
143B SER 3.6 2.8 + - - +
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Residues in contact with PHE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLN 5.3 1.6 - - - -
64B ARG* 4.7 3.4 - - + -
65B CYS* 3.7 39.9 - - + -
68B SER* 4.1 9.2 - - - -
69B VAL* 3.7 27.1 - - + -
72B ARG* 6.0 0.2 - - - -
138B ALA* 3.2 23.2 + - - +
139B THR 3.9 2.2 - - - -
140B GLU 3.3 0.2 - - - -
141B GLN* 1.3 111.9 - - + +
143B SER* 1.3 65.5 + - - +
144B ARG* 3.5 5.4 + - - +
410B GLU* 4.0 27.6 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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