Contacts of the strand formed by residues 175 - 181 (chain H) in PDB entry 2FGW
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 HIS 175 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173H GLY* 3.6 20.8 + - - -
174H VAL* 1.3 76.8 + - - +
176H THR* 1.3 62.6 + - - +
177H PHE* 3.7 12.3 + - + -
190H SER 3.3 2.6 - - - +
191H SER* 3.1 2.1 - - - -
192H VAL* 2.6 49.7 + - + +
193H VAL 6.1 0.2 - - - -
194H THR* 5.1 2.5 + - + -
135L LEU* 5.6 0.4 - - + -
137L ASN* 3.3 22.8 + - - -
138L ASN* 3.5 18.0 + - - -
164L THR* 4.3 12.5 + - + +
167L ASP* 5.6 6.7 - - + -
174L SER* 3.3 28.2 + - - -
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Residues in contact with THR 176 (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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161H VAL 5.5 1.6 - - - +
163H VAL* 4.4 17.7 + - + +
174H VAL* 4.0 9.5 + - - +
175H HIS* 1.3 74.0 - - - +
177H PHE* 1.3 66.0 + - - +
178H PRO* 3.9 4.3 - - - +
189H LEU* 3.7 34.1 - - + -
190H SER 3.3 3.4 - - - +
191H SER* 3.1 20.9 + - - +
164L THR* 4.7 6.1 - - - +
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Residues in contact with PHE 177 (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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175H HIS* 3.9 7.2 - - + -
176H THR* 1.3 77.6 - - - +
178H PRO* 1.3 70.4 - - - +
189H LEU* 3.6 18.5 - - - +
190H SER* 2.9 34.4 + - - +
192H VAL* 3.8 27.4 - - + -
135L LEU* 3.9 21.3 - - + -
162L SER* 3.1 33.4 - - - +
164L THR* 3.5 13.7 - - + -
174L SER* 3.3 29.2 - - - -
175L LEU 3.5 0.2 - - - -
176L SER* 3.3 34.3 - - - +
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Residues in contact with PRO 178 (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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176H THR 4.0 4.5 - - - +
177H PHE* 1.3 91.3 - - + +
179H ALA* 1.3 66.7 + - - +
180H VAL* 3.9 1.7 + - - +
188H SER 4.6 0.2 - - - +
189H LEU* 4.5 4.5 - - - -
162L SER* 3.4 19.8 + - - +
163L VAL 3.4 27.8 - - - +
164L THR* 4.3 7.2 - - - -
165L GLU 5.7 0.7 - - - +
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Residues in contact with ALA 179 (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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156H TYR* 3.2 27.8 - - + +
159H GLU* 3.9 15.5 + - - +
177H PHE 3.7 0.8 + - - -
178H PRO* 1.3 79.4 - - - +
180H VAL* 1.3 60.5 + - - +
181H LEU 3.9 1.6 + - - -
187H TYR* 3.9 18.4 - - + -
188H SER 3.6 11.7 - - - +
189H LEU* 4.1 8.0 - - + +
162L SER* 5.8 0.7 - - - -
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Residues in contact with VAL 180 (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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178H PRO 4.8 1.1 - - - +
179H ALA* 1.3 74.5 - - - +
181H LEU* 1.3 67.3 + - - +
182H GLN* 3.1 5.0 + - + +
187H TYR* 3.3 3.4 - - - -
188H SER* 3.1 33.9 + - - +
160L GLN* 3.2 45.8 - - + +
161L GLU 4.9 7.4 - - - +
162L SER* 4.6 19.3 - - - -
176L SER* 5.9 1.6 - - - +
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Residues in contact with LEU 181 (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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157H PHE* 4.9 5.2 - - + -
179H ALA 3.9 1.4 + - - -
180H VAL* 1.3 81.1 - - - +
182H GLN* 1.3 85.9 + - - +
183H SER 5.3 0.2 - - - +
185H GLY* 3.0 34.8 - - - +
186H LEU 4.2 0.2 - - - -
187H TYR* 3.4 47.8 - - + +
160L GLN* 3.6 2.3 - - - +
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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