Contacts of the strand formed by residues 180 - 189 (chain G) in PDB entry 6ALH
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 VAL 180 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47G LEU* 3.4 29.4 - - + +
48G LEU* 3.9 20.6 - - + +
51G MET* 5.7 1.1 - - + -
178G SER* 2.8 25.2 + - - +
179G PRO* 1.3 96.6 - - + +
181G GLU* 1.3 64.1 + - - +
183G ILE* 3.8 17.3 - - + -
205G MET* 5.0 6.1 - - - -
206G GLU 3.4 18.8 - - - +
207G THR* 4.2 9.4 - - + +
208G ASN 5.3 0.2 - - - +
211G ILE* 6.4 0.2 - - + -
216G ALA* 6.2 3.1 - - + -
821I ARG* 4.7 4.2 + - - -
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Residues in contact with GLU 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G LEU* 4.0 12.9 - - - +
180G VAL* 1.3 74.9 - - - +
182G ARG* 1.3 67.9 + - + +
183G ILE 4.0 0.7 + - - -
206G GLU* 3.8 11.0 + - + +
821I ARG* 2.9 63.8 + - - +
825I GLU* 5.3 4.2 - - - +
1091I GLY 5.0 0.2 - - - +
1093I PRO* 4.6 19.8 - - + +
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Residues in contact with ARG 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G HIS* 4.8 13.3 + - - -
181G GLU* 1.3 83.7 - - + +
183G ILE* 1.3 60.2 + - - +
204G GLU* 4.2 19.8 + - - +
205G MET* 3.4 3.5 + - - -
206G GLU* 2.7 69.0 + - + +
1090I ASN* 3.4 35.0 + - - +
1091I GLY* 3.3 24.7 - - - +
1092I THR* 3.8 24.2 - - + +
1093I PRO* 5.7 0.4 - - + -
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Residues in contact with ILE 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ARG* 3.4 51.0 + - + +
47G LEU* 4.8 15.5 - - + -
48G LEU* 3.7 30.9 - - + +
180G VAL* 3.8 28.5 - - + -
181G GLU 4.0 1.0 + - - -
182G ARG* 1.3 84.9 - - - +
184G ALA* 1.3 69.4 + - - +
185G TYR* 5.8 0.2 - - + -
203G ILE* 4.9 7.4 - - + -
204G GLU 3.7 1.8 - - - -
205G MET* 3.7 23.8 - - + -
206G GLU 4.2 0.2 - - - +
1091I GLY* 3.4 19.0 + - - +
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Residues in contact with ALA 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ARG* 4.9 1.6 - - - +
182G ARG* 5.7 0.4 - - + +
183G ILE* 1.3 78.1 - - - +
185G TYR* 1.3 71.3 + - - +
186G ASN* 5.3 4.9 - - - +
203G ILE* 3.5 8.1 - - - +
204G GLU* 2.8 42.3 + - + +
1087I TYR* 5.6 3.1 - - + -
1089I GLU 4.8 5.8 - - - +
1090I ASN 3.4 27.8 - - - +
1091I GLY* 3.7 5.6 - - - +
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Residues in contact with TYR 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G GLY 4.8 1.1 - - - -
37G HIS* 4.2 22.1 + + - -
40G GLY* 3.3 37.9 - - - -
41G ASN* 3.3 26.2 + - - +
44G ARG* 3.6 21.8 - - + -
184G ALA* 1.3 80.2 - - - +
186G ASN* 1.3 72.5 + - - +
187G VAL* 4.8 5.4 - - + -
201G LEU* 4.2 10.3 - - + -
202G VAL 3.3 10.1 - - - +
203G ILE* 4.0 15.5 - - + -
204G GLU* 5.9 0.2 - - - -
1087I TYR* 3.0 32.0 + + - -
1218I GLY* 3.4 15.3 + - - -
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Residues in contact with ASN 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184G ALA* 5.3 4.6 - - - +
185G TYR* 1.3 84.5 + - - +
187G VAL* 1.3 67.4 + - - +
188G GLU* 5.0 0.7 - - - +
200G LYS 3.9 0.5 - - - +
201G LEU* 4.5 0.4 - - - -
202G VAL* 2.8 43.6 + - + +
204G GLU* 4.6 15.0 + - - +
1089I GLU* 4.0 19.6 + - - +
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Residues in contact with VAL 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G GLY* 3.7 38.1 - - - +
37G HIS* 4.0 28.5 - - + +
185G TYR* 4.8 6.7 - - + -
186G ASN* 1.3 78.8 - - - +
188G GLU* 1.3 64.6 + - - +
199G ASP* 5.6 5.6 - - + -
200G LYS 3.7 4.9 - - - +
201G LEU* 3.8 17.7 - - + -
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Residues in contact with GLU 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G ASN 5.0 0.4 - - - +
187G VAL* 1.3 75.7 - - - +
189G ALA* 1.3 57.6 + - - +
199G ASP* 3.2 10.3 - - - +
200G LYS* 2.4 73.4 + - + +
202G VAL* 3.8 16.3 - - + +
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Residues in contact with ALA 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G GLU* 1.3 80.9 - - - +
190G ALA* 1.3 67.1 + - - +
197G ASP* 6.5 0.9 - - - -
198G LEU 3.4 8.5 - - - +
199G ASP* 4.4 2.9 - - - +
200G LYS* 3.3 21.7 + - - +
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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