Contacts of the strand formed by residues 187 - 196 (chain H) in PDB entry 6AL5
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 TYR 187 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H THR* 5.5 3.8 - - - +
121H THR* 4.4 16.9 + - + +
155H ASP* 3.1 10.4 + - - -
156H TYR* 2.7 63.6 + - + +
157H PHE* 3.9 25.6 - + - -
158H PRO* 4.7 0.7 - - + -
159H GLU* 3.9 40.4 - - + +
179H ALA* 4.3 11.9 - - + -
180H VAL 3.4 17.5 - - - -
181H LEU* 3.6 41.0 - - + +
186H LEU* 1.3 74.1 - - - +
188H SER* 1.3 61.3 + - - +
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Residues in contact with SER 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H LEU* 4.2 8.5 - - - +
153H VAL 3.4 10.4 + - - -
154H LYS* 3.5 24.9 - - - +
156H TYR* 3.9 2.0 - - - -
179H ALA* 3.3 1.6 - - - -
180H VAL* 2.9 39.2 + - - +
182H GLN* 3.6 26.9 - - - -
187H TYR* 1.3 77.4 - - - +
189H LEU* 1.3 61.8 + - - +
182L THR* 6.2 0.2 - - - +
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Residues in contact with LEU 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H LEU* 3.5 7.5 - - - +
153H VAL* 2.8 53.4 + - + -
156H TYR* 3.4 8.1 - - - +
161H VAL* 2.6 42.0 - - + +
163H VAL* 4.3 7.4 - - + -
176H THR* 4.0 17.9 - - + -
177H PHE 4.2 7.4 - - - +
178H PRO 5.0 1.8 - - - -
179H ALA* 3.9 17.5 - - + +
188H SER* 1.3 77.1 + - - +
190H SER* 1.3 96.2 + - - +
191H SER 3.9 1.6 - - - +
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Residues in contact with SER 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H LEU* 4.7 11.4 - - - -
151H CYS 3.4 8.5 - - - -
152H LEU* 4.4 11.4 - - - +
177H PHE* 3.0 38.6 + - - +
189H LEU* 1.3 87.4 - - - +
191H SER* 1.3 59.0 + - - +
192H VAL* 5.0 2.5 - - - -
137L VAL* 5.1 4.3 - - - +
180L SER* 3.2 27.8 + - - -
182L THR* 4.7 6.9 + - - -
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Residues in contact with SER 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H GLY* 3.1 1.9 - - - -
151H CYS* 2.7 40.7 + - - +
153H VAL* 6.0 0.2 - - - -
163H VAL* 3.7 26.3 - - - +
165H TRP* 3.6 18.4 + - - -
174H VAL* 4.3 1.2 - - - +
175H HIS 3.3 8.2 + - - -
176H THR* 2.7 29.2 + - - -
189H LEU* 3.9 1.9 - - - +
190H SER* 1.3 74.5 - - - +
192H VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H LEU* 4.3 15.3 - - + -
149H LEU 3.2 13.2 - - - +
150H GLY* 3.8 4.5 - - - -
165H TRP* 4.6 3.4 - - - -
174H VAL* 3.5 6.1 - - - +
175H HIS* 2.9 50.6 + - + +
177H PHE* 4.0 18.6 - - + -
190H SER* 5.0 3.6 - - - -
191H SER* 1.3 81.9 - - - +
193H VAL* 1.3 68.5 - - - +
194H THR* 6.2 0.7 - - + -
122L PHE* 5.0 4.3 - - + -
137L VAL* 5.9 1.8 - - + -
139L LEU* 3.5 36.3 - - + -
141L ASN* 5.2 1.8 - - - +
180L SER* 5.9 0.4 - - - -
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Residues in contact with VAL 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ALA 3.8 0.2 - - - +
148H ALA* 3.2 2.5 - - - -
149H LEU* 2.7 69.5 + - + +
165H TRP* 4.6 15.7 - - + -
170H LEU* 4.3 20.0 - - + -
172H SER 3.8 13.7 - - - +
173H GLY 3.3 15.9 - - - +
174H VAL* 4.0 12.6 - - + -
192H VAL* 1.3 79.6 - - - +
194H THR* 1.3 77.1 + - - +
195H VAL* 4.1 4.0 + - + -
205H TYR* 5.1 2.0 - - + -
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Residues in contact with THR 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H THR* 5.0 9.0 - - - +
147H ALA 3.0 7.0 - - - +
148H ALA* 3.8 21.5 - - + -
172H SER 4.5 4.7 - - - +
173H GLY* 3.3 17.0 + - - +
192H VAL* 6.2 0.7 - - + -
193H VAL* 1.3 83.7 - - - +
195H VAL* 1.3 65.6 + - - +
120L PHE* 4.3 8.5 - - + -
139L LEU* 5.6 1.6 - - + -
141L ASN* 3.1 33.8 + - - +
142L ASN* 5.2 1.9 + - - -
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Residues in contact with VAL 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H THR* 3.5 5.7 - - - -
147H ALA 2.6 47.7 + - - +
149H LEU* 4.0 18.8 - - + -
170H LEU* 5.4 6.3 - - + -
193H VAL* 5.0 4.3 - - + +
194H THR* 1.3 76.4 - - - +
196H PRO* 1.4 73.3 - - + +
199H SER* 4.4 0.7 - - - +
200H LEU* 3.6 29.2 - - + -
205H TYR* 2.8 36.1 - - + +
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Residues in contact with PRO 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H GLY 4.2 8.3 - - - +
146H THR* 4.4 8.0 - - + -
195H VAL* 1.4 96.4 - - + +
197H SER* 1.3 59.0 + - - +
198H SER* 3.1 16.4 - - - +
199H SER* 3.1 34.9 + - - +
200H LEU* 3.8 5.9 - - - +
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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