Contacts of the strand formed by residues 132 - 142 (chain C) in PDB entry 3DGG
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 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C GLN* 3.2 27.9 + - - +
128C LEU* 3.1 24.1 + - - +
130C SER* 3.5 3.0 + - - -
131C GLY* 1.3 79.9 - - - +
133C ALA* 1.3 61.1 + - - +
184C LEU 4.1 1.3 - - - -
185C THR* 5.1 0.9 - - - -
186C LYS* 4.3 3.1 - - - +
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Residues in contact with ALA 133 (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 PRO* 3.9 7.2 - - + -
127C GLN* 3.8 5.5 - - - +
128C LEU* 3.9 11.2 - - + -
132C GLY* 1.3 74.8 - - - +
134C SER* 1.3 62.0 + - - +
183C THR* 5.3 1.7 - - - +
184C LEU* 2.7 51.7 + - + +
185C THR 3.8 4.7 - - - +
186C LYS* 4.1 0.7 - - - -
189C TYR* 3.6 32.1 - - + -
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Residues in contact with SER 134 (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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122C PRO 4.1 1.0 - - - -
123C PRO* 3.3 23.9 - - - +
127C GLN* 2.8 34.3 + - - +
133C ALA* 1.3 74.8 - - - +
135C VAL* 1.3 62.4 + - - +
136C VAL* 4.1 4.2 + - - +
181C THR* 4.3 15.1 - - - +
182C LEU 3.6 4.5 - - - -
183C THR* 3.8 13.8 + - - +
130D LEU* 5.7 2.1 - - - +
147D LEU* 3.7 18.4 - - - +
149D LYS* 3.9 10.9 - - - +
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Residues in contact with VAL 135 (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 ILE* 4.4 2.7 - - + -
121C PHE 3.6 15.5 - - - +
123C PRO* 4.1 13.5 - - + -
134C SER* 1.3 75.8 - - - +
136C VAL* 1.3 60.4 + - - +
151C TRP* 3.5 33.0 - - + -
181C THR* 3.4 2.9 - - - +
182C LEU* 2.8 47.1 + - + +
184C LEU* 4.0 14.8 - - + -
189C TYR* 4.5 7.0 - - + -
195C TYR* 4.3 18.4 - - + -
212C PHE* 3.7 21.1 - - + -
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Residues in contact with VAL 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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120C ILE* 3.6 3.3 - - - +
121C PHE* 2.9 40.1 + - + -
134C SER 4.8 3.4 - - - +
135C VAL* 1.3 77.1 - - - +
137C CYS* 1.3 63.3 + - - +
138C PHE* 3.7 39.0 - - + -
151C TRP* 4.2 1.1 - - - -
179C SER* 4.1 10.1 - - - +
180C SER 3.6 3.8 - - - +
181C THR* 4.1 17.9 - - + +
130D LEU* 4.3 21.5 - - + -
147D LEU* 4.5 15.5 - - + -
184D SER* 4.1 12.6 - - - +
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Residues in contact with CYS 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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118C VAL* 3.7 18.2 - - - -
119C SER 3.3 4.7 - - - -
136C VAL* 1.3 75.7 - - - +
138C PHE* 1.3 63.0 + - - +
139C LEU* 3.9 14.1 + - - +
149C VAL* 5.4 1.1 - - - -
151C TRP* 3.5 19.3 - - + -
178C MET 4.0 0.2 - - - +
179C SER* 3.6 2.3 + - - -
180C SER* 2.8 43.6 + - - +
197C CYS* 2.0 47.8 - - + -
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Residues in contact with PHE 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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117C THR 3.4 0.7 - - - +
118C VAL* 3.2 7.4 - - - +
119C SER* 2.9 35.9 + - - +
121C PHE* 3.4 36.1 - + - -
136C VAL* 3.7 15.7 - - + -
137C CYS* 1.3 74.3 - - - +
139C LEU* 1.3 62.5 + - - +
140C ASN* 3.9 17.3 - - - +
178C MET 3.6 1.1 - - - -
179C SER* 3.7 19.1 - - - -
130D LEU* 4.2 5.2 - - + -
143D THR* 4.5 4.3 - - + -
144D LEU 4.2 0.2 - - - -
145D GLY* 4.0 12.3 - - - -
172D PHE* 3.5 31.9 - + - -
184D SER* 3.8 11.4 - - - -
185D SER 3.7 17.7 - - - -
186D SER* 3.5 21.1 - - - -
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Residues in contact with LEU 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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116C PRO* 4.2 11.0 - - + -
117C THR 3.7 2.5 - - - -
118C VAL* 3.2 39.0 - - + -
137C CYS* 3.9 12.8 - - - +
138C PHE* 1.3 79.8 - - - +
140C ASN* 1.3 59.7 + - - +
142C PHE* 3.1 18.6 - - + -
147C ILE* 4.6 8.5 - - + -
149C VAL* 3.3 37.2 - - + -
178C MET* 2.8 45.1 + - + +
180C SER* 5.6 0.9 - - - -
198C GLU 5.7 0.4 - - - -
199C ALA* 3.8 22.4 - - + +
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Residues in contact with ASN 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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116C PRO* 3.5 1.2 - - - +
117C THR* 2.9 44.5 + - - +
138C PHE* 3.9 12.9 - - - +
139C LEU* 1.3 76.8 - - - +
141C ASN* 1.3 78.3 + - + +
142C PHE 3.6 1.6 - - - -
177C SER* 3.4 18.1 - - - +
143D THR* 4.4 10.7 + - - +
170D HIS* 4.1 8.2 - - + -
172D PHE* 3.5 15.4 - - - -
186D SER* 3.1 28.6 + - - -
188D THR* 6.0 3.2 - - - -
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Residues in contact with ASN 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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114C ALA* 4.0 9.7 - - - +
115C ALA 3.7 10.9 - - - +
117C THR* 5.5 2.9 - - - +
140C ASN* 1.3 80.5 - - - +
142C PHE* 1.3 58.3 + - - +
170C ASP* 5.3 0.8 + - - -
173C ASP* 2.9 28.5 + - - -
175C THR* 3.4 21.4 + - + +
176C TYR 3.1 5.7 + - - -
177C SER* 2.8 13.3 + - - -
170D HIS* 2.9 32.7 + - - -
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Residues in contact with PHE 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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114C ALA* 3.2 14.8 - - - +
116C PRO* 3.6 27.8 - - + -
139C LEU* 3.1 28.7 - - + -
141C ASN* 1.3 74.3 - - - +
143C TYR* 1.3 63.1 + - - +
144C PRO 3.1 28.7 - - - -
145C LYS 3.4 15.3 - - - -
147C ILE* 3.8 30.5 - - + -
166C TRP* 3.8 15.7 - + - -
175C THR* 3.4 3.4 - - - -
176C TYR* 2.8 56.6 + - + +
177C SER* 3.6 5.4 - - - -
178C MET* 3.7 6.7 - - + -
201C HIS* 3.7 9.2 - + - +
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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