Contacts of the strand formed by residues 133 - 143 (chain A) in PDB entry 3KDM
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 THR 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLN* 3.2 41.7 + - - +
129A LEU* 3.9 6.8 + - - +
131A SER 3.7 4.5 + - - -
132A GLY* 1.3 82.4 + - - +
134A ALA* 1.3 61.9 + - - +
135A SER 4.1 0.2 - - - -
184A THR* 3.6 25.4 - - + -
185A LEU 2.8 25.1 - - - +
186A SER* 4.6 1.5 - - - +
187A LYS* 3.7 3.7 - - - +
152B LYS* 5.2 5.2 - - - -
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Residues in contact with ALA 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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124A PRO* 3.6 17.9 - - + -
129A LEU* 3.8 5.2 - - + -
133A THR* 1.3 74.6 - - - +
135A SER* 1.3 61.5 + - - +
136A VAL* 4.0 2.7 + - + +
183A LEU 3.5 3.5 - - - +
184A THR* 3.5 0.5 - - - -
185A LEU* 2.9 37.8 + - + +
186A SER 4.8 0.7 - - - +
187A LYS* 4.3 1.0 - - - +
190A TYR* 3.4 42.2 - - + -
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Residues in contact with SER 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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122A PHE 4.5 0.2 - - - +
123A PRO 4.3 0.9 - - - -
124A PRO* 3.4 22.2 - - - +
128A GLN* 2.8 29.3 + - - +
134A ALA* 1.3 72.4 - - - +
136A VAL* 1.3 61.0 + - - +
137A VAL* 4.1 3.4 + - - +
182A THR* 4.1 12.6 - - - +
183A LEU 3.4 5.2 - - - -
184A THR* 4.0 8.6 + - - +
133B LEU* 5.9 1.6 - - - +
150B LEU* 3.5 26.9 - - - +
152B LYS* 3.6 16.3 - - - +
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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
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121A ILE* 4.6 0.9 - - + -
122A PHE 3.4 16.6 - - - +
123A PRO* 4.5 0.9 - - + -
124A PRO* 4.7 11.2 - - + -
134A ALA 4.5 5.4 - - - +
135A SER* 1.3 77.4 - - - +
137A VAL* 1.3 60.5 + - - +
152A TRP* 3.6 27.2 - - + -
182A THR* 3.2 4.3 - - - -
183A LEU* 2.7 63.4 + - + +
185A LEU* 4.5 6.1 - - + -
190A TYR* 5.0 1.6 - - + -
196A TYR* 4.5 12.6 - - + -
213A PHE* 3.6 27.6 - - + -
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.5 1.9 - - - +
122A PHE* 2.7 56.6 + - + -
135A SER 4.8 1.8 - - - +
136A VAL* 1.3 78.0 - - - +
138A CYS* 1.3 70.1 + - - +
139A LEU* 5.4 1.3 - - + -
152A TRP* 3.8 2.9 - - - -
180A SER* 4.9 6.7 - - - -
181A SER 3.5 6.3 - - - +
182A THR* 3.8 22.7 - - + +
133B LEU* 3.8 30.1 - - + -
150B LEU* 4.6 9.4 - - + -
188B SER* 4.2 22.4 - - - +
190B VAL* 5.7 2.0 - - + -
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Residues in contact with CYS 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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119A VAL* 3.5 17.3 - - - -
120A PHE 3.2 15.0 - - - -
121A ILE* 4.8 0.9 - - + -
137A VAL* 1.3 78.2 - - - +
139A LEU* 1.3 58.0 + - - +
140A LEU* 4.1 10.1 - - - +
152A TRP* 3.5 17.4 - - + -
179A LEU 3.9 0.7 - - - +
180A SER* 3.5 3.5 - - - -
181A SER* 2.8 40.9 + - - +
198A CYS* 2.1 46.7 - - + -
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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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118A SER 3.3 1.0 - - - +
119A VAL* 3.2 9.0 - - - +
120A PHE* 2.8 57.2 + - + +
122A PHE* 4.2 11.9 - - + -
137A VAL* 4.2 2.1 - - + +
138A CYS* 1.3 71.5 - - - +
140A LEU* 1.3 73.2 + - - +
141A ASN* 3.9 26.5 - - + +
178A SER* 4.5 0.7 - - - -
179A LEU 3.5 2.2 - - - +
180A SER* 4.8 0.9 - - - +
146B ALA* 4.0 15.3 - - + -
175B PHE* 3.6 33.0 - - + -
190B VAL* 3.9 26.7 - - + -
192B THR* 4.8 2.0 - - + -
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Residues in contact with LEU 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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117A PRO* 3.9 9.2 - - + -
118A SER 3.7 3.8 - - - -
119A VAL* 4.5 1.1 - - + -
138A CYS* 4.1 13.0 - - - +
139A LEU* 1.3 77.7 - - - +
141A ASN* 1.3 59.0 + - - +
143A PHE* 3.3 18.3 - - + -
148A ALA* 4.2 16.6 - - + -
150A VAL* 3.6 28.5 - - + -
178A SER* 3.2 6.8 - - - -
179A LEU* 2.8 55.7 + - + +
181A SER 5.6 0.9 - - - +
200A VAL* 3.6 46.7 - - + -
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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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116A ALA 4.4 0.3 - - - +
117A PRO* 3.5 1.9 - - - +
118A SER* 2.8 45.0 + - - +
120A PHE* 4.2 6.8 - - + -
139A LEU* 3.9 24.7 - - + +
140A LEU* 1.3 72.7 - - - +
142A ASN* 1.3 93.9 + - - +
143A PHE* 3.7 1.8 - - - -
178A SER* 3.6 1.7 + - - -
171B SER 5.6 0.4 + - - -
173B HIS* 3.4 30.9 - - - -
190B VAL* 4.9 1.4 - - - +
192B THR* 3.9 25.5 + - - +
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Residues in contact with ASN 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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115A ALA* 3.9 9.0 - - - +
116A ALA 4.0 5.0 - - - +
118A SER* 6.0 0.2 - - - +
141A ASN* 1.3 93.1 + - - +
143A PHE* 1.3 57.4 + - - +
174A ASP* 4.2 11.4 + - - +
176A THR* 3.4 30.8 + - + +
177A TYR 3.2 5.7 + - - -
178A SER* 2.9 14.0 + - - -
171B SER* 5.8 2.4 + - - -
173B HIS* 2.9 29.6 + - - -
192B THR* 5.2 4.0 + - - -
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Residues in contact with PHE 143 (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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115A ALA* 3.2 16.2 - - - +
117A PRO* 3.6 34.1 - - + -
140A LEU* 3.3 35.4 - - + -
142A ASN* 1.3 74.4 - - - +
144A TYR* 1.3 62.9 + - - +
145A PRO 3.3 13.7 - - - -
146A ARG 3.5 24.9 - - - -
148A ALA* 4.4 9.6 - - + -
167A VAL* 5.2 3.4 - - + -
176A THR* 3.4 2.2 - - - -
177A TYR* 2.7 62.5 + - + -
178A SER* 3.8 3.1 - - - -
179A LEU* 3.8 17.7 - - + -
202A HIS* 3.5 13.2 - + - +
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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