Contacts of the strand formed by residues 135 - 145 (chain C) in PDB entry 3Q3G
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 135 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C GLN* 3.2 39.3 + - - +
131C LEU* 3.5 6.9 + - - +
133C SER* 3.4 5.2 + - - -
134C GLY* 1.3 80.2 - - - +
136C ALA* 1.3 62.0 + - - +
186C THR* 6.0 1.1 - - - -
187C LEU 4.2 7.2 - - - -
188C THR* 4.5 0.4 - - - -
189C LYS 4.3 0.7 - - - -
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Residues in contact with ALA 136 (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 PRO* 3.8 14.1 - - + -
130C GLN* 4.1 1.2 - - - +
131C LEU* 3.8 8.5 - - + -
135C GLY* 1.3 74.8 - - - +
137C SER* 1.4 59.5 + - - +
185C LEU 3.7 1.6 - - - +
186C THR* 3.5 1.1 - - - +
187C LEU* 2.8 41.6 + - + +
188C THR 3.6 9.2 - - - +
192C TYR* 3.5 38.4 - - + -
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Residues in contact with SER 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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124C PHE 4.3 0.2 - - - +
125C PRO 4.1 1.2 - - - +
126C PRO* 3.4 22.8 - - - +
130C GLN* 3.0 32.7 + - - +
136C ALA* 1.4 69.7 - - - +
138C VAL* 1.3 63.6 + - - +
139C VAL* 3.9 5.8 + - - +
184C THR* 4.0 12.8 - - - -
185C LEU 3.2 4.3 - - - -
186C THR* 3.0 30.5 + - - +
135D LEU* 5.4 1.6 - - - +
152D LEU* 4.1 11.9 - - - +
154D LYS* 3.7 4.3 - - - -
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Residues in contact with VAL 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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123C ILE* 4.0 5.6 - - + -
124C PHE 3.4 10.3 - - - +
126C PRO* 4.1 18.4 - - + -
137C SER* 1.3 74.1 - - - +
139C VAL* 1.3 60.0 + - - +
154C TRP* 3.6 31.2 - - + -
184C THR* 3.4 2.6 - - - -
185C LEU* 2.7 45.1 + - + +
187C LEU* 4.4 6.5 - - + -
192C TYR* 4.3 3.8 - - + -
198C TYR* 4.0 24.7 - - + -
215C PHE* 3.3 29.4 - - + -
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Residues in contact with VAL 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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123C ILE* 3.4 4.3 - - - +
124C PHE* 2.8 43.2 + - + -
137C SER 4.4 3.1 - - - +
138C VAL* 1.3 76.0 - - - +
140C CYS* 1.3 63.5 + - - +
141C PHE* 3.8 30.5 - - + -
154C TRP* 4.2 1.1 - - - -
182C SER* 4.2 2.7 - - - +
183C SER 3.5 7.2 - - - +
184C THR* 3.8 26.0 - - + +
135D LEU* 3.8 35.7 - - + -
152D LEU* 4.3 16.8 - - + -
189D SER* 4.9 2.7 - - - +
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Residues in contact with CYS 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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121C VAL* 3.8 6.7 - - - -
122C SER 3.2 4.5 - - - -
139C VAL* 1.3 75.6 - - - +
141C PHE* 1.3 62.5 + - - +
142C LEU* 3.6 26.0 - - - +
152C VAL* 4.9 2.7 - - - -
154C TRP* 3.6 18.2 - - + -
181C MET 3.9 0.5 - - - +
182C SER* 3.6 2.8 + - - -
183C SER* 2.8 41.3 + - - +
200C CYS* 2.0 47.8 - - + -
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Residues in contact with PHE 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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120C THR 3.3 2.0 - - - +
121C VAL* 3.2 5.7 - - - -
122C SER* 2.9 35.4 + - - +
124C PHE* 3.4 28.9 - + - -
139C VAL* 3.8 7.6 - - + -
140C CYS* 1.3 74.2 - - - +
142C LEU* 1.3 62.7 + - - +
143C ASN* 3.8 17.5 - - - +
181C MET 3.5 2.2 - - - -
182C SER* 3.6 20.0 - - - -
135D LEU* 3.8 17.3 - - + -
148D THR* 4.0 9.0 - - + -
149D LEU 4.2 0.9 - - - -
150D GLY* 3.9 14.6 - - - -
177D PHE* 3.6 27.6 - + - -
189D SER* 3.7 8.7 - - - -
190D SER 3.7 19.3 - - - -
191D SER* 3.8 18.8 - - - -
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Residues in contact with LEU 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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119C PRO* 4.1 11.2 - - + -
120C THR 3.7 4.3 - - - -
121C VAL* 3.7 16.6 - - + -
140C CYS* 3.6 25.6 - - - -
141C PHE* 1.3 76.9 - - - +
143C ASN* 1.3 58.6 + - - +
145C PHE* 3.3 18.2 - - + -
150C ILE* 3.9 21.3 - - + -
151C ASN 4.6 0.7 - - - +
152C VAL* 3.5 25.4 - - + -
180C SER* 3.3 0.2 - - - -
181C MET* 2.7 61.1 + - + +
201C GLU 6.0 0.2 - - - -
202C ALA* 3.8 18.6 - - + -
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Residues in contact with ASN 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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119C PRO* 3.5 1.2 - - - +
120C THR* 2.9 44.8 + - - +
122C SER* 5.8 0.2 + - - -
141C PHE* 3.8 11.4 - - - +
142C LEU* 1.3 75.9 - - - +
144C ASN* 1.3 80.7 + - - +
145C PHE* 3.5 2.5 - - - -
180C SER* 3.4 2.8 - - - +
148D THR* 3.9 18.6 + - - +
175D HIS* 2.8 25.4 + - - -
177D PHE* 3.4 16.1 - - - -
191D SER* 2.9 25.7 + - - -
193D THR* 4.6 4.2 + - - -
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Residues in contact with ASN 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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117C ALA* 3.7 11.6 - - - +
118C ALA 3.6 10.4 - - - +
120C THR* 5.1 5.4 + - - +
143C ASN* 1.3 87.3 + - - +
145C PHE* 1.3 57.2 + - - +
176C ASP* 3.0 24.0 + - - +
178C THR* 3.3 24.0 + - + +
179C TYR 3.2 5.1 + - - -
180C SER* 3.0 10.8 + - - -
628C EDO 3.2 31.8 + - - -
175D HIS* 3.7 6.8 - - - -
193D THR* 5.6 1.7 + - - -
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Residues in contact with PHE 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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117C ALA* 3.2 13.7 - - - +
119C PRO* 3.6 26.9 - - + -
142C LEU* 3.3 27.8 - - + -
144C ASN* 1.3 75.1 - - - +
146C TYR* 1.3 60.7 + - - +
147C PRO 3.3 14.1 - - - -
148C LYS 3.3 24.2 - - - -
150C ILE* 3.5 39.9 - - + -
169C TRP* 5.2 2.9 - + - -
178C THR* 3.8 1.3 - - - -
179C TYR* 2.8 65.2 + - + +
180C SER* 3.7 5.2 - - - -
181C MET* 3.8 12.3 - - + -
204C HIS* 3.8 7.2 - - - +
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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