Contacts of the strand formed by residues 164 - 173 (chain T) in PDB entry 6MZL
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 GLN 164 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162T VAL* 3.8 32.6 + - - +
163T PRO* 1.3 72.1 - - - +
165T LEU* 1.3 66.2 + - - +
166T GLN* 3.6 14.1 + - - +
260T GLY* 4.2 0.4 - - - -
261T SER 2.9 36.0 + - - +
262T CYS* 6.2 0.2 - - - -
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Residues in contact with LEU 165 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163T PRO 3.8 4.9 + - - +
164T GLN* 1.3 76.0 + - - +
166T GLN* 1.3 66.3 + - - +
167T ASN 4.8 3.1 - - - +
168T ILE* 4.0 8.5 - - + -
225T LYS* 3.5 46.5 - - - +
258T MET* 3.8 31.9 - - + -
259T VAL 3.9 12.8 - - - +
260T GLY* 4.4 7.6 - - - -
318T ARG* 3.4 44.0 - - + +
321T ILE* 4.7 17.3 - - + -
322T TYR* 5.7 0.9 - - + +
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Residues in contact with GLN 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE 4.8 6.7 - - - +
44A GLY* 4.6 6.1 - - - -
45A ASN* 5.9 0.5 + - - -
56A SER* 3.8 20.5 + - - -
58A LEU* 4.1 20.1 - - + +
164T GLN* 3.8 16.1 + - - +
165T LEU* 1.3 83.5 + - - +
167T ASN* 1.3 60.0 + - - +
223T GLY 4.6 3.8 - - - +
224T ALA 4.1 0.7 - - - +
225T LYS* 2.8 46.9 + - - +
259T VAL* 2.8 23.5 + - + +
260T GLY 4.4 0.4 - - - -
261T SER* 3.4 34.4 + - - +
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Residues in contact with ASN 167 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE 2.6 30.3 + - - -
42A LEU 2.7 22.4 + - - +
43A PHE 4.1 1.8 - - - +
44A GLY* 3.1 21.4 - - - +
165T LEU* 3.8 1.7 - - - +
166T GLN* 1.3 80.4 - - - +
168T ILE* 1.3 86.6 + - - +
169T VAL* 3.3 8.2 - - - +
222T THR* 4.0 3.4 - - - +
223T GLY* 3.0 24.1 + - - -
224T ALA 3.3 6.3 + - - -
225T LYS* 5.2 0.4 - - - -
258T MET* 3.5 1.1 - - - +
259T VAL* 2.9 32.9 + - + +
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Residues in contact with ILE 168 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165T LEU* 4.0 9.0 - - + -
167T ASN* 1.3 90.8 + - - +
169T VAL* 1.3 61.9 + - - +
221T CYS 3.9 5.0 - - - +
222T THR* 4.4 1.0 - - - -
223T GLY 4.2 5.2 + - - -
224T ALA 2.9 15.8 + - - +
225T LYS 4.8 0.2 - - - -
226T SER* 3.6 33.7 - - - +
227T GLU* 3.5 27.8 - - + +
230T SER* 4.1 22.9 + - - +
255T ILE* 3.7 34.5 - - + -
257T ASN 3.5 3.6 - - - -
258T MET* 3.8 21.5 - - + -
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Residues in contact with VAL 169 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.3 46.2 - - + +
42A LEU* 3.8 12.1 - - - +
81A LEU* 3.8 19.1 - - + -
167T ASN* 3.3 15.5 - - - +
168T ILE* 1.3 72.9 - - - +
170T SER* 1.3 55.7 + - - +
220T VAL* 4.4 6.5 - - + -
221T CYS 3.2 13.0 - - - +
222T THR* 4.6 0.2 - - + -
255T ILE* 3.6 1.6 - - - -
256T GLN* 2.6 36.3 + - + -
257T ASN* 2.8 26.8 + - + +
258T MET* 6.0 0.2 - - - -
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Residues in contact with SER 170 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168T ILE 4.1 0.4 + - - -
169T VAL* 1.3 75.9 - - - +
171T THR* 1.3 65.9 + - - +
220T VAL* 3.3 7.0 - - - +
221T CYS* 2.8 43.1 + - - +
230T SER* 3.0 24.3 + - - -
234T ALA* 4.6 0.9 - - - +
253T PHE* 3.4 24.3 - - - -
254T LYS 3.4 15.5 - - - -
255T ILE* 4.2 5.2 - - - -
256T GLN* 4.0 1.3 - - - +
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Residues in contact with THR 171 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLU 5.6 4.3 - - - +
81A LEU* 5.3 2.0 - - - +
170T SER* 1.3 80.9 - - - +
172T VAL* 1.3 65.0 + - - +
218T LYS* 6.4 1.1 - - - -
219T MET 3.3 7.2 - - - -
220T VAL* 3.8 28.0 - - + -
234T ALA* 6.4 0.2 - - - -
252T ASP 3.7 3.1 + - - +
253T PHE* 3.5 6.0 - - - -
254T LYS* 3.1 26.7 + - - +
256T GLN* 3.3 35.4 + - + +
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Residues in contact with VAL 172 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171T THR* 1.3 76.6 - - - +
173T ASN* 1.3 64.6 + - - +
174T LEU* 4.3 8.7 - - + -
217T GLY 4.0 0.2 - - - +
218T LYS* 3.3 5.0 - - - +
219T MET* 2.9 67.7 + - + +
234T ALA* 4.8 5.2 - - + -
250T PHE* 3.6 39.0 - - + -
251T LEU 3.4 21.8 - - - +
252T ASP 4.1 2.9 - - - -
253T PHE* 4.1 13.2 - - + -
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Residues in contact with ASN 173 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172T VAL* 1.3 74.5 - - - +
174T LEU* 1.3 67.7 + - - +
175T GLY* 3.2 17.1 + - - +
216T SER 4.8 2.4 - - - +
217T GLY* 3.3 14.8 - - - +
218T LYS* 3.8 25.3 - - + +
249T LYS 4.0 0.3 - - - +
251T LEU* 2.9 53.2 + - + +
252T ASP* 4.7 7.8 + - + +
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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