Contacts of the strand formed by residues 129 - 139 (chain M) in PDB entry 4DKE
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 129 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122I PHE* 5.7 2.0 - - + -
143I LYS* 3.7 27.1 + - - +
144I ASP* 5.4 0.4 - - - +
124M GLN* 2.8 38.6 - - + +
125M LEU* 4.1 4.5 + - - -
127M SER* 3.5 13.4 - - - +
128M GLY* 1.3 81.1 - - - +
130M ALA* 1.3 65.4 + - - +
131M SER* 5.6 0.2 + - - -
180M THR* 4.6 9.0 - - - +
181M LEU 3.5 12.5 + - - -
182M SER* 4.8 2.0 - - - +
183M LYS* 4.2 1.5 - - - +
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Residues in contact with ALA 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M PRO* 3.6 20.6 - - + -
124M GLN* 3.6 3.1 - - - -
125M LEU* 3.7 18.4 - - + -
129M THR* 1.3 77.4 + - - +
131M SER* 1.3 62.3 + - - +
132M VAL* 4.2 1.7 - - + +
179M LEU 3.9 0.5 - - - +
180M THR* 3.7 1.2 - - - +
181M LEU* 2.7 47.6 + - + +
182M SER 4.9 1.1 - - - +
183M LYS* 4.5 0.9 - - - +
186M TYR* 4.1 18.6 - - + -
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Residues in contact with SER 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I LEU* 5.6 2.1 - - - +
141I LEU* 3.6 24.3 - - - +
143I LYS* 3.9 20.8 - - - +
118M PHE 4.2 0.5 - - - +
119M PRO 4.2 1.4 - - - -
120M PRO* 3.6 20.5 - - - +
124M GLN* 3.2 23.3 + - - +
129M THR* 5.6 0.3 + - - -
130M ALA* 1.3 74.1 + - - +
132M VAL* 1.3 63.3 + - - +
133M VAL* 4.0 4.6 + - - +
178M THR* 4.5 8.4 - - - +
179M LEU 3.4 5.8 - - - -
180M THR* 4.2 10.0 + - - +
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Residues in contact with VAL 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M ILE* 3.5 22.2 - - + -
118M PHE 3.3 17.3 - - - +
120M PRO* 4.0 16.6 - - + -
130M ALA* 5.4 1.8 - - + +
131M SER* 1.3 75.3 - - - +
133M VAL* 1.3 61.2 + - - +
148M TRP* 3.6 18.2 - - + -
178M THR* 3.3 4.2 - - - +
179M LEU* 2.7 54.1 + - + +
181M LEU* 5.0 11.2 - - + -
186M TYR* 5.0 5.8 - - + -
192M TYR* 5.0 6.3 - - + -
209M PHE* 4.1 19.1 - - + -
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Residues in contact with VAL 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 3.8 34.5 - - + -
141I LEU* 4.3 17.5 - - + -
179I SER* 4.7 10.5 - - - +
181I VAL* 6.0 2.7 - - + -
117M ILE* 3.5 3.0 - - - -
118M PHE* 3.0 53.1 + - + -
131M SER 4.6 2.2 - - - +
132M VAL* 1.3 76.5 - - - +
134M CYS* 1.3 67.7 + - - +
135M LEU* 5.1 3.6 - - + -
176M SER* 5.4 7.0 - - - +
177M SER 3.8 2.7 - - - +
178M THR* 3.6 21.8 - - + +
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Residues in contact with CYS 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M VAL* 4.1 13.2 - - - -
116M PHE 3.3 15.0 - - - -
117M ILE* 4.3 2.2 - - + -
133M VAL* 1.3 74.4 - - - +
135M LEU* 1.3 59.8 - - - +
136M LEU* 4.6 6.2 - - - +
148M TRP* 3.7 17.8 - - + -
175M LEU 3.8 2.1 - - - +
176M SER* 3.9 2.8 - - - -
177M SER* 3.0 34.5 + - - +
194M CYS* 2.0 52.3 - - + -
196M VAL* 4.6 2.9 - - - -
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Residues in contact with LEU 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I ALA* 4.4 9.6 - - + -
166I PHE* 3.5 32.1 - - + -
181I VAL* 3.6 31.4 - - + -
183I THR* 5.7 0.4 - - + -
114M SER 3.3 5.5 - - - +
115M VAL* 3.4 3.2 - - - +
116M PHE* 2.9 56.7 + - + -
118M PHE* 4.5 10.8 - - + -
133M VAL* 5.1 4.0 - - + -
134M CYS* 1.3 75.0 - - - +
136M LEU* 1.3 81.0 + - - +
137M ASN* 4.2 16.8 - - + +
175M LEU 3.7 2.9 - - - +
176M SER* 5.0 1.1 - - - +
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Residues in contact with LEU 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M PRO* 3.9 17.5 - - + -
114M SER 3.7 2.9 - - - -
115M VAL* 5.3 1.3 - - + -
134M CYS* 4.6 9.2 - - - +
135M LEU* 1.3 80.7 - - - +
137M ASN* 1.3 59.7 + - - +
139M PHE* 3.8 17.5 - - + -
144M ALA* 4.0 25.4 - - + -
146M VAL* 4.0 17.7 - - + -
174M SER* 3.1 6.6 - - - -
175M LEU* 2.9 60.4 + - + +
177M SER 5.5 0.2 - - - +
196M VAL* 3.8 37.7 - - + -
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Residues in contact with ASN 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I GLY 5.8 0.2 + - - -
164I HIS* 3.1 16.3 - - - -
181I VAL* 5.0 1.7 - - - +
183I THR* 3.6 28.5 + - - +
113M PRO* 3.5 2.5 - - - +
114M SER* 2.9 50.5 + - - +
116M PHE* 4.5 2.5 - - + -
135M LEU* 4.2 20.0 - - + +
136M LEU* 1.3 73.7 - - - +
138M ASN* 1.3 96.5 + - - +
139M PHE* 3.6 2.0 - - - -
174M SER* 3.0 18.0 + - - -
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Residues in contact with ASN 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I HIS* 3.2 23.2 + - - -
183I THR* 5.6 1.6 + - - -
111M ALA* 4.1 6.8 - - - +
112M ALA 3.9 8.7 - - - +
114M SER* 5.3 2.4 + - - +
137M ASN* 1.3 95.6 - - - +
139M PHE* 1.3 56.7 + - - +
170M ASP* 4.3 10.9 + - - +
172M THR* 3.2 31.0 + - + +
173M TYR 3.0 6.9 + - - -
174M SER* 2.9 13.5 + - - -
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Residues in contact with PHE 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M ALA* 3.2 14.8 - - - +
113M PRO* 3.6 22.9 - - + -
136M LEU* 3.6 33.9 - - + -
137M ASN 4.2 0.7 - - - -
138M ASN* 1.3 75.2 - - - +
140M TYR* 1.3 61.6 + - - +
141M PRO 3.3 26.7 - - - -
142M ARG* 3.6 21.1 - - - -
144M ALA* 4.3 9.6 - - + -
163M VAL* 5.5 2.0 - - + -
172M THR* 3.7 2.6 - - - -
173M TYR* 2.9 48.4 + - + -
174M SER* 3.5 24.9 - - - -
175M LEU* 4.0 19.7 - - + -
198M HIS* 3.8 10.3 - + - -
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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