Contacts of the strand formed by residues 128 - 138 (chain G) in PDB entry 5IXM
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 TYR 128 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114G PHE* 5.2 0.5 - - - -
126G ASP* 3.5 15.2 - - - +
127G GLY* 1.3 84.3 + - - +
129G ALA* 1.3 69.5 + - - +
130G THR* 3.4 21.3 + - - -
151G PHE* 4.1 17.0 - + - -
152G GLN 3.2 16.4 - - - +
153G VAL* 3.7 15.0 - - + +
154G PHE* 3.5 17.6 - - - -
64H GLN* 6.0 0.3 + - - -
108H ASP* 3.4 31.4 + - - -
109H ASN 4.4 2.2 - - - -
110H PRO* 3.5 32.5 - - + -
113H ALA* 4.2 13.3 + - + +
116H LYS* 4.8 10.2 - - - +
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Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G THR* 3.5 34.3 - - + +
107G ARG* 4.9 0.4 - - - -
108G VAL* 5.2 1.3 - - + -
114G PHE* 5.1 3.1 - - + -
128G TYR* 1.3 77.0 - - - +
130G THR* 1.3 61.8 + - - +
131G GLN* 4.5 0.5 - - - +
151G PHE* 3.4 8.3 - - - +
152G GLN* 2.9 46.4 + - + +
154G PHE* 4.0 12.8 - - + -
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Residues in contact with THR 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ASN* 3.1 33.3 + - - +
105G TYR 3.6 0.2 - - - -
106G THR* 2.9 28.7 + - - -
128G TYR* 3.4 22.3 - - - -
129G ALA* 1.3 73.1 - - - +
131G GLN* 1.3 63.0 + - - +
132G ILE* 3.9 20.0 - - + -
151G PHE* 3.8 20.3 - - + -
117H GLU* 5.1 4.2 + - - +
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Residues in contact with GLN 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ASN 3.5 1.8 - - - -
105G TYR* 3.4 36.9 + - + -
106G THR 3.1 28.5 + - - +
107G ARG* 3.7 23.8 - - - +
129G ALA 4.5 0.9 - - - +
130G THR* 1.3 73.6 - - - +
132G ILE* 1.3 61.7 + - - +
133G PHE* 4.8 3.5 - - + -
148G SER 3.6 3.3 - - - +
150G GLN* 2.9 71.4 + - + +
151G PHE 4.4 0.5 + - - -
152G GLN* 3.8 22.0 + - - +
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Residues in contact with ILE 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G ASN 5.3 1.1 - - - +
103G ILE* 3.6 4.3 - - - +
104G ASN* 2.9 50.8 + - + +
105G TYR* 4.4 0.6 - - - +
130G THR* 3.9 18.8 - - + -
131G GLN* 1.3 80.4 - - - +
133G PHE* 1.3 66.8 + - - +
134G THR* 4.0 18.6 - - - +
148G SER 3.2 5.6 - - - +
149G LYS* 3.9 29.2 - - + -
150G GLN 4.7 0.9 - - - +
151G PHE* 4.5 4.7 - - + -
117H GLU* 3.8 36.8 - - + +
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Residues in contact with PHE 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89G TRP* 4.2 16.2 - + - -
102G ASN 3.9 2.0 - - - -
103G ILE* 4.0 37.0 - - + -
105G TYR* 3.4 44.4 - + + -
131G GLN* 4.8 2.0 - - + -
132G ILE* 1.3 76.9 - - - +
134G THR* 1.3 64.0 + - - +
146G LEU 4.6 0.2 - - - -
147G SER* 3.1 6.6 - - - -
148G SER* 2.9 49.8 + - - +
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Residues in contact with THR 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G ARG* 4.8 3.8 - - + +
101G PHE* 3.4 4.7 - - - +
102G ASN* 2.9 63.5 + - + +
103G ILE* 5.2 1.7 - - - +
132G ILE* 4.0 11.2 - - - +
133G PHE* 1.3 75.6 + - - +
135G ALA* 1.3 65.4 + - - +
145G THR* 3.7 23.3 - - + -
146G LEU 3.5 4.0 - - - -
147G SER* 3.1 14.9 + - - -
149G LYS* 5.7 0.7 - - - -
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Residues in contact with ALA 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G ARG 3.3 5.4 - - - -
101G PHE* 3.7 25.1 - - + -
134G THR* 1.3 78.8 - - - +
136G GLY* 1.3 57.0 + - - +
145G THR* 4.6 0.2 - - - -
146G LEU* 2.9 38.6 + - + +
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Residues in contact with GLY 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G VAL 3.7 0.3 - - - +
99G TRP* 3.6 11.1 - - - -
100G ARG* 2.9 41.2 + - - +
101G PHE* 5.1 1.4 - - - -
134G THR* 5.0 0.6 - - - +
135G ALA* 1.3 76.0 - - - +
137G TYR* 1.3 60.5 + - - -
144G ALA 3.2 13.2 - - - -
145G THR* 4.0 8.3 - - - +
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Residues in contact with TYR 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G VAL* 3.3 43.0 - - + +
99G TRP* 4.0 34.5 - + + -
100G ARG* 5.1 0.4 - - - -
136G GLY* 1.3 74.5 - - - -
138G ALA* 1.3 73.9 + - - +
139G ASN* 3.2 39.2 + - - +
142G TRP* 3.7 33.2 - + + -
143G ASN* 3.2 2.3 - - - +
144G ALA* 2.9 36.0 + - + +
145G THR* 5.0 0.5 + - - -
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Residues in contact with ALA 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G VAL* 3.0 31.3 + - - +
100G ARG* 3.8 24.5 - - - -
137G TYR* 1.3 82.7 - - - +
139G ASN* 1.3 60.1 + - - +
142G TRP 3.6 6.7 - - - -
143G ASN* 3.6 14.8 - - + +
25H TYR* 3.4 27.1 - - + +
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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