Contacts of the strand formed by residues 198 - 203 (chain A) in PDB entry 4YZU
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 PRO 198 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TRP* 4.1 16.2 - - + +
30A GLN* 3.2 30.5 - - - +
44A GLY 3.9 2.5 - - - +
45A SER* 3.1 24.9 - - - +
137A TYR 3.6 1.3 - - - +
138A VAL* 3.4 21.3 - - - -
139A SER* 3.6 11.4 + - - +
197A GLY* 1.3 87.1 - - - +
199A HIS* 1.3 57.3 + - - +
200A VAL* 3.8 20.0 - - + -
209A LEU* 4.0 4.3 - - + -
211A GLY 3.9 4.5 - - - +
213A ILE* 3.7 7.9 - - - +
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Residues in contact with HIS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 4.0 10.5 - - + -
135A SER 5.1 0.9 - - - -
136A GLY* 3.9 28.1 + - - -
137A TYR 3.4 4.0 - - - -
138A VAL* 3.8 22.7 - - + -
160A VAL* 4.0 15.9 + - + +
162A LEU* 6.1 0.8 + - - -
181A PHE* 3.6 33.4 - + - -
183A ALA* 4.8 1.6 - - - +
198A PRO* 1.3 72.5 - - - +
200A VAL* 1.3 59.9 + - - +
201A THR* 4.2 2.5 - - - -
209A LEU* 3.7 3.3 - - - +
210A THR* 2.8 55.2 + - - -
211A GLY* 2.9 27.9 + - - +
228A TYR* 4.0 12.3 - + + -
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 5.2 3.6 - - + -
29A TRP* 3.8 14.4 - - + +
121A ILE* 3.6 30.7 - - + -
136A GLY* 3.1 4.7 - - - -
137A TYR* 2.8 59.0 + - + +
198A PRO* 3.8 22.9 - - + -
199A HIS* 1.3 79.3 + - - +
201A THR* 1.3 63.2 + - - +
202A GLU* 4.3 1.9 + - + +
207A SER* 4.1 18.8 - - - +
208A PHE 3.2 9.2 - - - +
209A LEU* 4.3 2.0 - - + -
210A THR* 3.6 1.1 - - - -
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 3.5 28.9 + - + +
131A LEU* 4.6 1.0 + - - -
133A PHE* 3.8 22.4 - - + -
135A SER 4.0 19.4 + - - +
199A HIS* 4.2 5.0 - - - -
200A VAL* 1.3 74.2 + - - +
202A GLU* 1.3 66.9 + - - +
203A VAL* 3.7 6.5 + - + +
206A THR 3.7 0.2 - - - +
207A SER* 3.5 1.9 - - - -
208A PHE* 2.9 30.6 + - - +
210A THR* 2.9 31.0 + - - +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 5.4 5.0 - - - -
133A PHE* 4.6 5.9 - - - -
135A SER 5.1 1.4 + - - -
137A TYR* 4.0 39.7 + - + +
200A VAL* 5.3 2.3 - - + +
201A THR* 1.3 78.6 - - - +
203A VAL* 1.3 62.3 + - - +
204A GLU 3.9 1.9 + - - -
205A GLY* 5.1 8.3 - - - +
206A THR 3.7 7.0 - - - +
207A SER* 3.6 18.9 + - - +
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 3.8 42.6 - - + -
133A PHE* 4.1 14.6 - - + -
201A THR* 3.9 7.9 - - + +
202A GLU* 1.3 77.4 - - - +
204A GLU* 1.3 73.1 + - + +
206A THR* 2.8 27.4 + - - +
208A PHE* 3.7 26.9 - - + -
96B GLU* 3.6 23.5 - - - +
97B GLN* 4.7 4.8 - - + +
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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