Contacts of the strand formed by residues 136 - 149 (chain C) in PDB entry 6UML
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 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C VAL 3.2 13.7 - - - -
123C LEU* 4.3 3.4 - - - -
135C PHE* 1.3 78.8 - - - +
137C THR* 1.3 67.9 + - - -
164C ARG* 3.6 3.5 - - - +
165C PHE* 3.0 41.2 + - - +
299C LEU* 4.5 6.2 - - - +
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Residues in contact with THR 137 (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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91C LEU* 3.0 43.4 + - + +
93C PRO* 3.9 15.1 - - + +
122C VAL* 2.9 34.3 + - - +
136C GLY* 1.3 77.0 + - - -
138C THR* 1.3 73.4 + - - +
139C ALA* 3.6 0.7 + - - +
162C ARG 4.1 2.0 - - - +
163C GLN 3.2 24.1 + - - +
164C ARG* 4.3 1.6 - - - +
165C PHE* 3.3 7.3 - - - -
299C LEU* 3.7 14.6 - - - +
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Residues in contact with THR 138 (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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73C HIS* 6.0 4.9 - - + -
81C ILE* 3.9 22.4 - - + -
119C THR* 5.3 8.3 - - - -
120C PHE 3.4 9.4 - - - -
137C THR* 1.3 73.6 - - - +
139C ALA* 1.3 55.9 + - - +
161C GLY* 3.3 4.2 - - - -
162C ARG* 2.7 40.1 + - - +
163C GLN* 2.7 43.4 + - + +
165C PHE* 3.5 22.9 - - + -
184C ILE* 4.5 7.2 - - + -
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Residues in contact with ALA 139 (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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91C LEU* 4.7 4.9 - - + -
97C LEU* 4.8 4.0 - - + -
119C THR* 3.2 3.4 - - - -
120C PHE* 2.7 66.7 + - + -
122C VAL* 4.0 12.1 - - + -
137C THR 3.6 0.4 + - - -
138C THR* 1.3 73.9 - - - +
140C GLU* 1.3 59.3 + - - +
159C ALA* 3.8 11.0 - - + -
160C ILE 3.5 11.2 - - - +
161C GLY* 4.5 3.1 - - - +
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Residues in contact with GLU 140 (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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69C GLY* 3.3 25.1 - - - -
71C THR* 3.0 40.3 + - - +
117C ASP 4.5 0.7 - - - +
118C ARG* 3.4 11.0 + - - +
119C THR* 3.5 18.3 - - + +
138C THR 4.3 0.2 - - - -
139C ALA* 1.3 72.3 - - - +
141C ILE* 1.3 71.4 + - - +
142C TYR* 3.4 3.0 + - + +
159C ALA* 3.1 3.6 - - - -
160C ILE* 2.9 33.3 + - + +
162C ARG* 2.7 47.1 + - + +
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Residues in contact with ILE 141 (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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67C PHE* 5.2 4.3 - - + +
110C VAL* 3.9 28.3 - - + -
113C LEU* 5.0 8.3 - - + -
114C ILE* 5.3 8.3 - - + -
118C ARG* 2.9 51.3 + - + +
120C PHE* 3.8 30.7 - - + -
140C GLU* 1.3 74.6 - - - +
142C TYR* 1.3 58.4 + - - +
143C ALA 3.4 29.6 - - - +
144C TYR* 4.3 8.5 - - + -
157C VAL* 4.0 17.3 - - + -
158C LYS 3.7 4.5 - - - +
159C ALA* 3.9 4.0 - - + +
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Residues in contact with TYR 142 (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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55C THR 4.7 3.6 + - - -
57C HIS* 4.4 5.4 - - - -
67C PHE* 3.2 44.0 + - - +
69C GLY* 6.0 2.9 - - - +
96C THR* 3.4 25.2 + - - -
118C ARG* 5.7 0.9 - - - +
140C GLU* 3.4 4.2 + - + +
141C ILE* 1.3 73.5 - - - +
143C ALA* 1.3 65.5 + - + +
158C LYS* 2.9 75.7 + - + +
159C ALA 3.9 4.9 - - - -
160C ILE* 3.7 28.5 - - + -
162C ARG* 5.8 1.8 - - - +
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Residues in contact with ALA 143 (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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67C PHE* 3.9 10.8 - - + +
141C ILE* 3.4 8.2 - - - +
142C TYR* 1.3 93.1 - - + +
144C TYR* 1.3 65.5 + - - +
157C VAL* 3.4 0.6 - - - -
158C LYS* 3.0 47.7 + - - +
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Residues in contact with TYR 144 (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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67C PHE* 3.9 24.2 - + + -
110C VAL* 4.5 9.4 - - + -
111C ARG* 5.1 10.6 - - + +
114C ILE* 4.2 25.4 - - + -
141C ILE* 4.3 7.4 - - + -
143C ALA* 1.3 78.7 - - - +
145C ARG* 1.3 65.2 + - - +
146C GLU* 2.6 39.6 + - + +
155C VAL* 3.5 33.4 - - + +
156C LYS 3.4 7.4 - - - +
157C VAL* 3.8 12.6 - - + -
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Residues in contact with ARG 145 (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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144C TYR* 1.3 79.3 - - - +
146C GLU* 1.3 61.2 + - - +
147C GLU* 3.8 6.2 + - + +
155C VAL* 3.7 1.9 - - - -
156C LYS* 3.0 45.7 + - + +
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Residues in contact with GLU 146 (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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107C VAL* 4.8 8.1 - - - +
111C ARG* 5.3 6.5 - - - +
144C TYR* 2.6 36.4 + - + +
145C ARG* 1.3 71.1 - - - +
147C GLU* 1.3 62.6 + - - +
148C GLN* 3.8 19.5 + - + +
153C GLU* 5.9 5.0 - - + +
154C ILE 3.7 4.3 - - - +
155C VAL* 4.0 20.7 - - + +
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Residues in contact with GLU 147 (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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145C ARG* 3.8 6.2 + - + +
146C GLU* 1.3 73.7 - - - +
148C GLN* 1.3 58.7 + - - +
149C ASP* 3.1 45.0 - - - +
153C GLU* 3.7 1.4 - - - +
154C ILE* 2.7 58.1 + - + +
156C LYS* 4.2 19.9 + - + +
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Residues in contact with GLN 148 (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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146C GLU* 3.8 19.9 + - + +
147C GLU* 1.3 75.0 - - - +
149C ASP* 1.3 59.4 + - - +
151C GLY* 4.1 9.3 + - - -
152C ILE 3.5 8.7 - - - +
153C GLU* 4.1 26.5 - - + +
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Residues in contact with ASP 149 (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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147C GLU* 3.1 36.8 - - - +
148C GLN* 1.3 75.0 - - - +
150C PHE* 1.3 92.3 + - + +
151C GLY 3.1 4.6 + - - -
152C ILE* 3.5 13.8 + - - +
154C ILE* 3.6 14.1 - - - +
156C LYS* 5.8 0.6 + - - -
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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
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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