Contacts of the strand formed by residues 130 - 140 (chain M) in PDB entry 2ZPK
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 LYS 130 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I LYS* 3.6 27.6 - - - +
125M GLU* 3.2 19.9 + - - +
126M LEU* 3.4 13.7 - - - +
128M THR* 3.2 22.8 - - - +
129M ASN* 1.3 92.5 - - - +
131M ALA* 1.3 61.8 + - - +
132M THR* 5.5 0.2 - - - +
181M LEU 3.7 7.8 + - - +
182M THR* 4.3 17.8 - - - +
183M ALA 3.9 2.2 - - - +
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Residues in contact with ALA 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M PRO* 4.0 9.4 - - + -
125M GLU* 3.7 2.7 - - - -
126M LEU* 3.6 11.7 - - + -
130M LYS* 1.3 77.7 - - - +
132M THR* 1.3 62.1 + - - +
133M LEU* 5.0 1.3 - - + -
179M LEU 3.6 1.7 - - - +
180M THR* 3.5 1.6 - - - -
181M LEU* 2.7 49.1 + - + +
182M THR 3.9 2.7 - - - +
186M TRP* 3.6 32.3 - - + -
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Residues in contact with THR 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 5.5 1.6 - - - +
141I LEU* 3.9 13.8 - - + +
143I LYS* 4.0 9.1 + - + +
176I THR* 6.1 0.4 - - + -
120M PRO 4.1 1.9 - - - +
121M PRO* 3.5 20.2 - - - +
125M GLU* 2.6 35.8 + - - +
130M LYS* 5.5 0.2 - - - +
131M ALA* 1.3 73.9 - - - +
133M LEU* 1.3 74.4 + - - +
134M VAL* 4.1 10.0 + - + +
178M TYR* 3.9 21.8 - - + -
179M LEU 3.3 3.4 - - - +
180M THR* 3.7 27.8 - - + +
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Residues in contact with LEU 133 (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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118M LEU* 4.2 14.4 - - + -
119M PHE 3.5 8.7 - - - +
121M PRO* 4.0 9.9 - - + -
131M ALA 4.8 1.3 - - - +
132M THR* 1.3 80.4 - - - +
134M VAL* 1.3 60.7 + - - +
135M CYS 4.1 0.4 - - - -
149M TRP* 3.9 19.1 - - + -
177M SER 3.9 0.3 - - - +
178M TYR* 3.4 6.1 - - - -
179M LEU* 2.9 35.6 + - + +
181M LEU* 3.8 28.5 - - + -
186M TRP* 4.1 19.3 - - + -
192M TYR* 3.4 36.1 - - + -
207M LEU* 4.4 11.7 - - + -
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Residues in contact with VAL 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 4.2 27.1 - - + -
141I LEU* 4.1 15.5 - - + -
178I SER* 3.7 19.3 - - - +
117M THR 3.5 1.9 - - - +
118M LEU* 3.4 4.4 - - - -
119M PHE* 2.8 42.3 + - + -
132M THR* 4.1 7.6 - - + +
133M LEU* 1.3 76.5 - - - +
135M CYS* 1.3 62.5 + - - +
136M THR* 4.0 21.8 - - + -
176M SER* 5.1 1.3 - - - -
177M SER 3.7 2.7 - - - +
178M TYR* 3.7 27.6 - - + -
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Residues in contact with CYS 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M VAL* 3.6 24.7 - - - -
117M THR 3.3 6.5 - - - -
118M LEU* 4.3 2.0 - - + -
133M LEU 4.1 0.6 - - - -
134M VAL* 1.3 72.1 - - - +
136M THR* 1.3 62.7 + - - +
137M ILE* 4.3 4.0 - - - +
149M TRP* 3.7 16.6 - - + -
176M SER* 3.2 4.9 - - - -
177M SER* 2.8 41.8 + - - +
194M CYS* 2.0 50.5 - - + -
196M VAL* 4.4 3.8 - - - -
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Residues in contact with THR 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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124I LEU* 5.7 0.7 - - + -
137I THR* 5.1 1.6 - - - +
166I PHE* 3.6 33.4 - - + -
178I SER* 5.1 3.6 - - - -
179I SER 6.0 0.2 - - - -
180I SER* 4.8 9.0 + - - -
115M SER 3.6 1.6 - - - +
116M VAL* 3.4 6.1 - - - +
117M THR* 2.8 51.8 + - - +
119M PHE* 4.1 16.2 - - + -
134M VAL* 4.0 18.8 - - + -
135M CYS* 1.3 74.8 - - - +
137M ILE* 1.3 66.5 + - - +
138M THR* 5.1 2.4 - - - +
175M ALA 3.9 3.4 - - - -
176M SER* 4.8 2.2 - - - -
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Residues in contact with ILE 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I PHE* 4.0 1.0 - - - -
114M PRO* 3.5 30.1 - - + -
115M SER 3.4 2.9 - - - -
116M VAL* 4.2 3.8 - - + -
135M CYS* 4.3 10.5 - - - +
136M THR* 1.3 83.5 - - - +
138M THR* 1.3 61.9 + - - +
140M PHE* 3.6 15.9 - - + -
145M VAL* 4.6 2.7 - - + -
147M VAL* 3.6 34.1 - - + -
162M THR* 5.4 0.2 - - + -
174M MET* 3.1 3.5 - - - -
175M ALA* 2.8 56.1 + - + +
176M SER* 4.9 2.2 - - - +
177M SER 5.0 1.8 - - - +
196M VAL* 3.8 28.7 - - + -
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Residues in contact with THR 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I HIS* 3.6 25.7 + - + -
166I PHE* 3.5 26.9 - - + -
180I SER* 5.1 1.6 - - - +
114M PRO* 3.5 1.7 - - - +
115M SER* 2.9 43.5 + - - +
136M THR* 5.1 2.5 - - - +
137M ILE* 1.3 82.3 - - - +
139M ASP* 1.3 80.8 + - - +
140M PHE* 3.3 5.0 + - - -
168M GLN* 3.3 11.7 - - - +
173M TYR 3.5 2.2 - - - -
174M MET* 4.2 0.4 - - + -
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Residues in contact with ASP 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I HIS* 4.2 9.9 + - - -
112M SER* 2.7 29.1 + - - +
113M SER 3.4 8.8 - - - +
115M SER* 4.6 8.1 - - - -
138M THR* 1.3 88.0 + - - +
140M PHE* 1.3 56.4 + - - +
168M GLN* 2.8 41.2 + - - +
170M ASN* 3.3 15.3 + - - -
172M LYS* 3.5 16.9 - - + +
173M TYR 3.0 2.6 + - - -
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Residues in contact with PHE 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M SER 3.2 10.1 - - - +
114M PRO* 3.8 17.7 - - + -
137M ILE* 3.6 40.4 - - + -
138M THR 3.3 3.8 - - - -
139M ASP* 1.3 79.5 - - - +
141M TYR* 1.3 64.7 + - - +
142M PRO 3.4 18.4 - - - -
143M GLY* 3.8 16.6 - - - -
145M VAL* 3.6 31.6 - - + -
165M PRO* 4.0 15.0 - - + -
172M LYS* 3.6 1.1 - - - +
173M TYR* 2.9 69.9 + - + +
174M MET* 3.7 7.0 - - - -
175M ALA* 3.8 3.8 - - + -
198M HIS* 3.9 6.3 - - + -
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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