Contacts of the strand formed by residues 109 - 127 (chain C) in PDB entry 3M4D
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 THR 109 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ILE* 4.0 8.1 - - + +
108C ASP* 1.3 81.5 - - - +
110C LYS* 1.3 66.6 + - - +
148C TYR* 3.3 22.3 - - - -
149C VAL 5.2 0.5 + - - -
149D VAL* 3.7 23.6 - - + +
150D GLN 3.6 6.7 - - - -
151D PRO* 3.7 20.0 - - + -
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Residues in contact with LYS 110 (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 THR* 1.3 80.3 - - - +
111C GLU* 1.3 60.8 + - - +
146C LEU* 3.8 23.6 - - + -
147C LYS 3.6 13.2 - - - +
148C TYR* 4.0 14.1 - - + +
149D VAL* 3.5 6.0 - - - +
150D GLN* 2.8 49.7 + - - +
151D PRO 3.5 6.3 + - - -
152D ASP* 2.8 25.8 + - - +
173D ASN* 2.6 42.2 + - - -
174D MET* 4.4 2.7 - - - +
175D VAL* 4.1 8.5 - - + -
181D PRO* 3.9 15.0 - - + -
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Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LYS* 1.3 75.1 - - - +
112C TYR* 1.3 63.0 + - - +
113C ASN* 3.1 30.1 + - - +
145C THR 3.7 0.4 - - - +
146C LEU* 3.5 10.9 - - - +
147C LYS* 2.9 59.4 + - + +
147D LYS* 4.0 13.5 + - - +
148D TYR 3.7 15.9 - - - +
149D VAL* 4.4 12.9 - - + +
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Residues in contact with TYR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LYS 4.2 0.2 + - - -
111C GLU* 1.3 74.8 - - - +
113C ASN* 1.3 73.2 + - - +
114C SER* 3.2 26.0 - - - -
144C HIS* 3.0 34.5 + - + +
145C THR 3.5 11.2 - - - -
146C LEU* 4.9 4.5 - - + -
146D LEU 3.7 0.9 - - - +
147D LYS* 3.5 1.2 - - - -
148D TYR* 3.0 49.6 + + + +
150D GLN* 3.7 26.0 - - - +
180D GLY 4.0 8.5 + - - -
181D PRO* 3.7 31.9 - - + -
178E ASN* 3.6 23.8 + - - -
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Residues in contact with ASN 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLU* 3.1 31.8 + - - +
112C TYR* 1.3 99.9 + - - +
114C SER* 1.3 63.4 + - - +
115C THR* 5.2 1.3 - - - +
143C GLY 4.5 0.2 - - - -
144C HIS* 3.2 4.7 - - - +
145C THR* 2.8 53.3 + - - +
147C LYS* 3.7 19.9 + - - -
145D THR* 4.6 7.0 - - + -
146D LEU 3.1 6.3 - - - +
147D LYS* 3.5 29.9 - - + +
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Residues in contact with SER 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C TYR* 3.2 28.9 - - - -
113C ASN* 1.3 70.3 - - - +
115C THR* 1.3 62.5 + - - +
142C ILE* 6.2 0.7 - - - -
143C GLY 3.3 5.6 - - - -
144C HIS* 3.3 15.4 + - - -
144D HIS* 3.8 1.4 - - - +
145D THR* 3.1 3.1 - - - -
146D LEU* 2.8 45.5 + - - +
148D TYR* 4.9 0.5 + - - -
178E ASN* 4.0 18.5 + - - +
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Residues in contact with THR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ASN* 5.2 1.7 - - - +
114C SER* 1.3 76.4 - - - +
116C LEU* 1.3 62.1 + - - +
117C THR* 3.5 20.6 - - - +
141C SER 3.7 0.7 - - - +
142C ILE* 3.2 7.3 - - - +
143C GLY* 2.7 46.3 + - - +
143D GLY 5.4 0.9 - - - -
144D HIS 3.3 7.6 - - - +
145D THR* 2.6 31.2 + - - +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C SER 4.3 0.2 - - - -
115C THR* 1.3 72.3 - - - +
117C THR* 1.3 63.7 + - - +
118C TYR* 4.7 13.2 - - + -
140C VAL* 3.9 18.8 - - + -
141C SER 3.4 15.0 - - - +
142C ILE* 3.6 24.0 - - + -
142D ILE 4.0 0.7 - - - +
143D GLY* 3.1 3.1 - - - -
144D HIS* 3.0 60.1 + - + +
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Residues in contact with THR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C THR* 3.5 18.4 - - - +
116C LEU* 1.3 78.1 + - - +
118C TYR* 1.3 70.5 + - - +
139C ASN* 4.3 4.1 - - - +
140C VAL* 3.2 3.8 - - - +
141C SER* 2.7 51.2 + - - -
141D SER* 4.6 12.1 - - - +
142D ILE 3.6 13.0 - - - +
143D GLY* 4.1 7.2 - - - +
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Residues in contact with TYR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 4.7 17.7 - - + -
117C THR* 1.3 79.6 - - - +
119C GLY* 1.3 59.0 + - - +
120C PHE* 4.5 25.1 - + + -
139C ASN* 3.1 14.1 - - - +
140C VAL* 3.9 15.3 - - + -
141D SER* 3.3 4.6 - - - -
142D ILE* 2.9 81.8 + - + +
143D GLY* 5.0 0.7 - - - -
144D HIS* 5.3 6.5 - + - -
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Residues in contact with GLY 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C TYR* 1.3 76.6 - - - +
120C PHE* 1.3 75.3 + - - -
138C ALA* 3.2 0.9 - - - -
139C ASN* 2.9 48.7 + - - +
140D VAL 3.2 11.2 - - - -
141D SER* 3.9 6.1 - - - -
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Residues in contact with PHE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C TYR* 4.5 27.8 - + + -
119C GLY* 1.3 85.8 - - - -
121C ASN* 1.3 65.2 + - - +
136C ILE* 6.6 0.2 - - + -
137C GLY 3.5 6.5 - - - +
138C ALA* 3.8 18.8 - - + -
139C ASN 5.5 0.9 - - - -
139D ASN* 3.3 1.6 - - - +
140D VAL* 2.9 41.6 + - + +
142D ILE* 6.4 1.3 - - + -
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Residues in contact with ASN 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASN* 5.5 2.0 + - - -
119C GLY 5.1 0.3 - - - +
120C PHE* 1.3 77.9 - - - +
122C GLY* 1.3 65.4 + - - +
123C ASN* 5.4 3.4 - - - +
135C LEU* 5.5 6.1 + - - +
136C ILE* 3.5 6.5 - - - +
137C GLY* 2.9 52.7 + - - +
138C ALA* 4.6 1.4 - - - -
139C ASN* 5.3 4.0 + - - -
138D ALA 3.2 15.7 - - - +
139D ASN* 3.5 12.8 - - + +
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Residues in contact with GLY 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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121C ASN* 1.3 80.4 + - - +
123C ASN* 1.3 67.2 + - - +
135C LEU 3.2 8.5 - - - -
136C ILE* 4.6 6.1 - - - -
137D GLY* 3.4 3.2 - - - -
138D ALA* 2.9 31.4 + - - +
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Residues in contact with ASN 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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121C ASN* 5.4 3.1 - - - +
122C GLY* 1.3 73.3 - - - +
124C VAL* 1.3 64.7 + - - +
125C THR* 3.5 13.6 + - - +
134C GLY* 3.1 5.5 - - - -
135C LEU* 2.7 64.2 + - + +
121D ASN* 4.9 3.6 + - - -
135D LEU* 2.9 49.2 - - - +
136D ILE 3.8 4.5 - - - -
137D GLY* 3.8 10.4 - - - -
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Residues in contact with VAL 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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123C ASN* 1.3 77.0 - - - +
125C THR* 1.3 67.4 + - - +
132C ILE* 4.5 11.7 - - + -
133C GLY 3.3 9.9 - - - +
134C GLY* 5.2 2.7 - - - -
135D LEU* 3.0 16.7 - - - +
136D ILE* 3.0 28.6 + - + +
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Residues in contact with THR 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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123C ASN* 3.5 13.9 - - - +
124C VAL* 1.3 75.7 - - - +
126C GLY* 1.3 60.1 + - - +
132C ILE* 3.4 10.4 - - - +
133C GLY* 2.8 49.9 + - - +
134C GLY 5.5 0.9 - - - +
135C LEU* 6.2 0.2 - - + -
134D GLY 3.7 7.6 - - - -
135D LEU* 3.3 28.7 - - + -
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Residues in contact with GLY 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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125C THR* 1.3 78.9 - - - +
127C ASP* 1.3 61.6 + - - +
131C LYS 3.1 13.2 - - - -
132C ILE* 4.0 10.8 - - - -
133D GLY* 3.4 2.8 - - - -
134D GLY* 3.0 30.6 + - - +
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Residues in contact with ASP 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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126C GLY* 1.3 74.7 - - - +
128C ASP* 1.3 62.1 + - - +
129C THR* 2.5 27.9 + - - +
130C GLY* 2.9 22.2 + - - -
131C LYS* 2.7 52.3 + - - +
132C ILE* 5.1 0.9 - - - +
131D LYS* 4.4 15.7 + - + +
132D ILE 3.6 8.7 - - - +
133D GLY* 4.4 4.0 - - - -
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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