Contacts of the strand formed by residues 132 - 142 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A GLN* 3.2 32.0 + - - +
128A LEU* 3.3 16.5 + - - +
130A SER* 3.5 2.4 + - - -
131A GLY* 1.3 79.1 - - - +
133A ALA* 1.3 63.2 + - - +
184A LEU 3.9 4.0 - - - -
185A THR* 4.7 0.9 - - - -
186A LYS 3.9 2.9 - - - -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO* 4.0 7.9 - - + -
127A GLN* 3.8 5.0 - - - +
128A LEU* 3.8 9.6 - - + -
132A GLY* 1.3 75.1 - - - +
134A SER* 1.3 61.2 + - - +
135A VAL* 5.3 0.7 - - - -
182A LEU 3.7 1.9 - - - +
183A THR* 3.5 3.0 - - - +
184A LEU* 2.8 48.1 + - + +
185A THR 3.8 4.3 - - - +
189A TYR* 3.5 36.1 - - + -
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PHE 4.4 0.2 - - - +
122A PRO 4.2 0.5 - - - -
123A PRO* 3.4 22.3 - - - +
127A GLN* 2.9 32.6 + - - +
133A ALA* 1.3 71.2 - - - +
135A VAL* 1.3 61.5 + - - +
136A VAL* 3.9 5.5 + - - +
181A THR* 3.8 14.1 - - - +
182A LEU 3.4 4.5 - - - -
183A THR* 3.1 17.2 + - - +
130B LEU* 5.5 1.6 - - - +
147B LEU* 3.6 21.7 - - - +
149B LYS* 4.0 8.7 + - - +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ILE* 4.2 4.0 - - + -
121A PHE 3.4 16.6 - - - +
123A PRO* 4.0 15.7 - - + -
133A ALA 5.1 0.9 - - - +
134A SER* 1.3 75.2 - - - +
136A VAL* 1.3 59.9 + - - +
151A TRP* 3.3 32.3 - - + -
181A THR* 3.4 2.0 - - - -
182A LEU* 2.8 42.6 + - + +
184A LEU* 4.8 6.1 - - + -
189A TYR* 4.1 17.0 - - + -
195A TYR* 4.2 16.2 - - + -
212A PHE* 3.6 21.3 - - + -
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 3.5 3.6 - - - +
121A PHE* 2.8 41.6 + - + +
134A SER 4.5 4.9 - - - +
135A VAL* 1.3 75.3 - - - +
137A CYS* 1.3 65.1 + - - +
138A PHE* 3.8 28.9 - - + -
151A TRP* 4.3 0.9 - - - -
179A SER* 5.4 0.9 - - - -
180A SER 3.7 2.9 - - - +
181A THR* 4.0 24.5 - - + +
130B LEU* 3.7 36.1 - - + -
147B LEU* 4.3 20.9 - - + -
184B SER* 4.7 4.7 - - - +
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Residues in contact with CYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL* 3.9 11.9 - - - -
119A SER 3.4 4.5 - - - -
120A ILE* 4.5 0.9 - - + +
136A VAL* 1.3 74.7 - - - +
138A PHE* 1.3 64.7 + - - +
139A LEU* 3.8 20.8 - - - +
149A VAL* 5.0 0.7 - - - -
151A TRP* 3.6 18.4 - - + -
179A SER* 3.4 4.2 - - - -
180A SER* 2.8 40.9 + - - +
197A CYS* 2.1 47.3 - - - -
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Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR 3.5 0.7 - - - +
118A VAL* 3.3 6.8 - - - +
119A SER* 2.9 42.2 + - - +
121A PHE* 3.5 33.0 - + - -
136A VAL* 3.8 17.9 - - + -
137A CYS* 1.3 73.4 - - - +
139A LEU* 1.3 60.7 - - - +
140A ASN* 3.9 16.4 - - - +
178A MET 3.7 1.1 - - - -
179A SER* 3.8 8.5 - - - -
130B LEU* 4.4 4.0 - - + -
143B THR* 4.5 0.9 - - + -
144B LEU 4.5 0.2 - - - -
145B GLY* 4.1 12.3 - - - -
172B PHE* 3.4 35.7 - + - -
184B SER* 3.6 22.2 - - - -
185B SER 3.7 18.2 - - - -
186B SER* 3.7 20.4 - - - -
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO* 4.1 11.4 - - + -
117A THR 3.8 3.1 - - - -
118A VAL* 4.4 9.0 - - + +
137A CYS* 3.8 29.6 - - - +
138A PHE* 1.3 76.8 - - - +
140A ASN* 1.3 60.6 + - - +
142A PHE* 3.2 16.3 - - + -
147A ILE* 4.1 6.3 - - + -
149A VAL* 3.5 33.7 - - + -
177A SER* 3.5 0.2 - - - -
178A MET* 2.7 47.2 + - + +
180A SER* 4.4 6.5 - - - +
198A GLU 5.1 0.2 - - - -
199A ALA* 3.3 36.1 - - + +
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Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PRO* 3.5 1.2 - - - +
117A THR* 2.9 42.3 + - - +
119A SER* 5.5 0.2 + - - -
138A PHE* 4.0 11.7 - - - +
139A LEU* 1.3 79.7 + - - +
141A ASN* 1.3 81.9 + - - +
142A PHE* 3.5 2.0 - - - -
177A SER* 3.6 9.3 - - - +
143B THR* 4.8 8.1 + - - +
170B HIS* 4.0 9.1 - - - -
172B PHE* 3.5 23.7 - - - -
186B SER* 3.1 29.3 + - - -
188B THR* 5.0 5.7 + - - -
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Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ALA* 3.9 10.0 - - - +
115A ALA 3.8 8.7 - - - +
117A THR* 5.4 4.6 + - - +
140A ASN* 1.3 81.8 - - - +
142A PHE* 1.3 58.5 + - - +
170A ASP* 4.7 2.0 + - - -
173A ASP* 3.9 11.4 + - - +
175A THR* 3.1 30.2 + - + +
176A TYR 3.1 5.2 + - - -
177A SER* 3.0 10.1 + - - -
170B HIS* 3.2 33.8 + - - -
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Residues in contact with PHE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ALA* 3.3 16.8 - - - +
116A PRO* 3.6 29.6 - - + -
139A LEU 3.2 28.0 - - - -
141A ASN* 1.3 73.8 - - - +
143A TYR* 1.3 63.7 + - - +
144A PRO 3.3 15.7 - - - -
145A LYS 3.3 24.5 - - - -
147A ILE* 3.6 32.8 - - + -
166A TRP* 5.1 3.1 - + - -
175A THR* 3.6 1.9 - - - -
176A TYR* 2.8 65.0 + - + +
177A SER* 3.8 9.2 - - - -
178A MET* 3.9 10.3 - - + -
201A HIS* 3.9 7.4 - + - +
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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