Contacts of the strand formed by residues 122 - 132 (chain C) in PDB entry 4LML
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 SER 122 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C ASP* 5.3 2.8 - - - +
117C ARG* 5.8 1.0 - - - +
120C PHE 3.8 1.8 + - - -
121C ASP* 1.3 75.6 - - - +
123C GLN* 1.3 73.5 + - - +
162C GLU* 4.8 0.7 + - - -
188C ARG* 5.7 6.5 - - - -
189C ILE 3.7 9.2 - - - -
190C SER* 3.3 21.7 - - - +
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Residues in contact with GLN 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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112C PRO 3.9 6.9 + - - -
113C LEU* 3.5 27.4 - - + +
114C ASP* 2.7 56.3 + - - +
121C ASP* 3.2 13.4 - - - +
122C SER* 1.3 79.8 - - - +
124C THR* 1.3 69.4 + - - +
125C LEU* 4.0 1.3 - - + -
159C TRP* 3.9 23.0 - - + -
188C ARG* 3.7 6.1 + - - +
189C ILE* 2.8 44.1 + - + +
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Residues in contact with THR 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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111C SER* 4.5 1.9 + - - -
112C PRO* 4.8 3.1 - - - +
123C GLN* 1.3 80.7 + - - +
125C LEU* 1.3 65.0 + - - +
126C HIS* 3.9 30.1 + - + +
186C GLN* 4.2 8.5 + - - +
187C LEU 3.7 4.9 + - - -
188C ARG* 3.4 51.4 + - - +
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Residues in contact with LEU 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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29C LEU* 3.5 24.7 - - + -
36C PHE* 3.5 42.4 - - + -
111C SER* 3.8 17.5 - - - +
112C PRO 4.4 1.3 - - - +
113C LEU* 3.6 31.4 - - + -
123C GLN* 4.8 1.8 - - + -
124C THR* 1.3 76.3 + - - +
126C HIS* 1.3 62.3 + - - +
156C LEU* 4.5 5.8 - - + -
186C GLN* 3.4 6.2 - - - -
187C LEU* 2.9 45.0 + - + +
189C ILE* 3.7 18.6 - - + -
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Residues in contact with HIS 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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36C PHE* 4.0 1.0 - - - -
79C ASN* 3.0 19.3 + - - +
109C VAL* 3.1 12.3 - - - +
111C SER* 3.1 18.0 + - - +
112C PRO* 5.0 11.7 - - + -
124C THR* 3.9 32.1 + - + +
125C LEU* 1.3 77.2 + - - +
127C ILE* 1.3 65.5 + - - +
128C TYR* 3.2 38.9 + + + -
184C ASP* 3.2 25.8 + - - +
185C TYR 3.4 2.5 + - - -
186C GLN* 4.0 12.9 - - + +
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ILE* 4.4 12.1 - - + -
23C LEU* 5.3 5.4 - - + -
36C PHE* 3.7 23.3 - - + -
38C VAL* 4.0 19.7 - - + -
77C PHE* 3.7 30.3 - - + -
79C ASN* 3.9 3.6 - - - +
105C PHE* 5.8 0.2 - - + -
109C VAL* 3.7 22.9 - - + -
125C LEU 5.7 0.4 - - - -
126C HIS* 1.3 80.3 - - - +
128C TYR* 1.3 63.2 + - - +
129C LEU* 3.8 10.3 - - + -
164C PHE* 5.4 7.0 - - + -
185C TYR* 2.9 47.7 + - + +
187C LEU* 5.8 4.7 - - + +
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Residues in contact with TYR 128 (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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153A ASP* 5.6 7.4 - - + -
77C PHE* 3.6 6.8 - - - +
78C VAL* 3.0 49.0 + - + -
79C ASN* 3.3 34.9 + - + +
126C HIS* 3.2 40.8 + + + -
127C ILE* 1.3 73.8 - - - +
129C LEU* 1.3 63.4 + - - +
182C LYS* 4.1 24.0 - - + -
183C LEU 3.3 7.2 - - - +
184C ASP* 3.4 38.2 + - + -
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Residues in contact with LEU 129 (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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19C THR* 4.5 17.0 - - + -
21C ILE* 4.1 7.6 - - + -
42C LEU* 3.8 32.5 - - + -
75C ILE* 4.6 11.7 - - + -
76C ARG 3.7 3.1 - - - +
77C PHE* 3.8 24.5 - - + -
127C ILE* 3.8 25.4 - - + +
128C TYR* 1.3 80.8 - - - +
130C ILE* 1.3 61.1 + - - +
140C VAL* 4.2 6.3 - - + +
181C SER 3.6 1.0 - - - +
182C LYS* 3.4 2.0 - - - -
183C LEU* 2.9 39.2 + - + +
185C TYR* 3.9 23.1 - - + -
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Residues in contact with ILE 130 (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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24A ILE* 6.2 2.2 - - + -
41A PHE* 5.9 0.7 - - + -
104A ARG* 5.0 3.4 - - - +
75C ILE* 3.7 7.4 - - - +
76C ARG* 2.9 76.3 + - + +
78C VAL* 3.7 26.2 - - + -
128C TYR 4.1 0.8 + - - -
129C LEU* 1.3 72.6 - - - +
131C VAL* 1.3 63.6 + - - +
140C VAL* 5.2 1.6 - - - -
173C PHE* 6.0 1.3 - - + -
180C GLU* 3.4 27.4 - - + +
181C SER 3.0 13.7 - - - +
182C LYS* 3.5 26.0 - - + -
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Residues in contact with VAL 131 (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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17C VAL* 5.7 1.3 - - + -
73C PRO* 4.9 4.3 - - + -
74C GLU 3.7 17.5 - - - +
75C ILE* 3.7 18.6 - - + -
76C ARG* 5.6 2.5 - - - +
130C ILE* 1.3 76.9 - - - +
132C ARG* 1.3 70.9 + - - +
133C SER* 5.2 0.2 + - - -
138C ASN* 4.0 31.6 - - + +
139C ILE 4.9 0.2 - - - +
140C VAL* 3.6 25.1 - - + +
179C LEU 4.1 0.2 - - - +
180C GLU* 3.1 10.2 - - - +
181C SER* 3.0 42.4 + - - -
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Residues in contact with ARG 132 (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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41A PHE* 5.1 3.0 - - - -
89A VAL* 3.7 26.2 - - + +
90A ASP* 4.9 6.4 + - - +
102A LEU* 3.4 27.6 - - - +
74C GLU* 4.6 4.3 + - - +
76C ARG* 4.7 11.0 - - - +
131C VAL* 1.3 83.8 - - - +
133C SER* 1.3 70.9 + - - +
134C VAL* 5.3 1.7 - - - +
138C ASN* 4.6 3.4 - - - +
175C LEU* 2.9 24.2 + - - +
176C GLU* 3.2 25.5 + - - +
178C ARG* 3.3 31.0 - - + +
179C LEU 3.9 1.3 - - - +
180C GLU* 3.5 34.8 + - + +
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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