Contacts of the strand formed by residues 172 - 181 (chain L) in PDB entry 3HI6
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 172 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H HIS* 5.8 0.4 - - - -
12L SER* 5.6 0.5 + - - -
104L GLU* 2.5 37.0 + - - +
137L ASN* 3.2 5.6 + - - -
138L PHE* 2.8 54.8 + - + +
139L TYR* 3.8 25.3 - + - -
141L ARG* 3.6 49.8 - - + -
162L VAL* 4.1 10.1 - - + -
163L THR* 3.5 20.9 - - - -
165L GLN* 3.4 40.7 + - + -
171L THR* 1.3 75.0 - - - +
173L SER* 1.3 62.2 + - - +
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Residues in contact with SER 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H HIS* 3.3 24.3 + - - -
173H PHE* 3.6 15.2 - - - -
135L LEU 3.3 9.4 - - - -
136L ASN* 3.1 22.8 + - - -
137L ASN* 3.1 13.0 + - - -
138L PHE* 3.7 2.5 - - - -
162L VAL* 3.4 6.2 - - - +
163L THR* 3.0 38.9 + - - -
172L TYR* 1.3 72.7 + - - +
174L LEU* 1.3 63.1 + - - +
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Residues in contact with LEU 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H PHE* 3.5 6.0 - - - -
134L LEU* 3.6 4.9 - - - +
135L LEU* 2.8 47.2 + - + +
138L PHE* 3.7 22.7 - - + -
141L ARG 5.3 2.7 - - - +
143L ALA* 4.8 14.4 - - + +
145L VAL* 4.0 24.5 - - + -
160L GLU* 3.6 22.0 - - - +
161L SER 3.4 11.2 - - - +
162L VAL* 3.6 22.7 - - + -
173L SER* 1.3 77.0 - - - +
175L SER* 1.3 77.8 + - - +
176L SER* 3.8 5.4 - - - +
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Residues in contact with SER 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H PHE* 3.5 27.4 - - - +
186H SER* 5.1 6.6 + - - -
132L VAL* 4.7 9.6 - - - -
133L CYS 3.4 7.4 - - - -
134L LEU* 4.8 1.3 - - - +
159L GLN 3.8 0.9 + - - +
160L GLU* 3.2 4.3 - - - -
161L SER* 2.9 43.9 + - - -
174L LEU* 1.3 79.6 - - - +
176L SER* 1.3 58.3 + - - +
177L THR* 4.2 12.0 + - - -
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Residues in contact with SER 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L VAL* 3.6 1.2 - - - -
133L CYS* 2.9 37.2 + - - +
145L VAL* 3.7 28.4 + - - +
147L TRP* 2.8 31.1 + - - -
158L SER* 4.2 5.7 + - - -
159L GLN 3.4 6.3 + - - -
160L GLU* 4.2 15.2 + - - +
174L LEU* 3.8 4.4 - - - +
175L SER* 1.3 73.6 - - - +
177L THR* 1.3 62.9 + - - +
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Residues in contact with THR 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H LEU* 5.3 7.7 - - + +
150H LYS* 6.4 0.2 - - - -
184H SER* 6.1 0.2 - - - +
186H SER* 5.1 2.8 + - - -
130L SER* 4.1 22.7 - - - +
131L VAL 3.4 8.7 - - - +
132L VAL* 4.1 18.8 - - + +
158L SER* 3.0 7.0 - - - -
159L GLN* 2.8 39.3 + - - +
175L SER* 4.4 10.2 + - - -
176L SER* 1.3 74.3 + - - +
178L LEU* 1.3 64.6 + - - +
179L THR* 3.9 9.8 + - - +
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Residues in contact with LEU 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L ALA 3.6 1.4 - - - +
130L SER* 3.3 5.9 - - - -
131L VAL* 2.8 52.4 + - + +
147L TRP* 3.7 44.3 - - + -
149L VAL* 4.1 19.5 - - + -
154L GLN* 4.4 4.0 - - + -
157L ASN* 3.4 46.4 - - - +
158L SER* 4.3 3.6 - - - -
176L SER 4.1 1.2 + - - -
177L THR* 1.3 71.6 - - - +
179L THR* 1.3 60.0 + - - +
180L LEU* 4.1 25.1 - - + -
191L TYR* 4.7 2.2 - - + -
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Residues in contact with THR 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H LYS* 5.6 8.5 - - - +
178H GLN* 5.6 2.4 + - - +
128L THR* 4.9 13.2 - - + -
129L ALA 3.6 5.4 - - - +
130L SER* 4.8 6.7 + - - +
157L ASN* 2.9 29.7 + - - +
158L SER* 5.8 0.2 - - - -
159L GLN* 5.7 0.5 + - - -
177L THR* 4.5 12.8 + - - +
178L LEU* 1.3 74.9 + - - +
180L LEU* 1.3 77.9 + - - +
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Residues in contact with LEU 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L THR* 3.4 8.7 - - - -
129L ALA 2.8 35.1 + - - +
131L VAL* 4.4 6.3 - - + -
149L VAL* 4.8 4.3 - - + -
154L GLN* 4.2 7.9 - - - +
157L ASN* 3.6 27.4 - - - +
178L LEU* 4.1 19.7 - - + -
179L THR* 1.3 78.4 - - - +
181L SER* 1.3 66.2 + - - +
184L ASP* 4.5 12.8 - - + +
185L TYR* 4.3 20.6 - - + +
188L HIS* 6.5 0.2 - - + -
191L TYR* 3.7 30.7 - - + -
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Residues in contact with SER 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127L GLY 3.4 10.5 - - - -
128L THR* 4.3 3.4 - - - +
129L ALA 4.4 1.3 - - - -
180L LEU* 1.3 76.5 - - - +
182L LYS* 1.3 59.2 + - - +
183L ALA* 3.7 8.7 + - - +
184L ASP* 3.0 34.8 + - - +
185L TYR* 2.8 27.5 + - - +
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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