Contacts of the strand formed by residues 207 - 212 (chain A) in PDB entry 4WMJ
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 ALA 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ILE* 4.4 1.1 - - - -
155A ASP* 3.5 5.8 - - + -
157A ILE* 3.9 17.5 - - + -
202A LEU* 4.1 15.9 - - + -
203A ASN 3.3 14.3 + - - +
204A PRO* 3.7 8.1 + - + +
205A GLU 3.7 0.2 - - - -
206A THR* 1.3 79.1 - - - +
208A LEU* 1.3 57.6 + - - +
209A PHE* 4.0 16.0 + - + -
231A TRP* 4.9 0.2 - - + -
245A HIS* 2.8 35.4 - - - +
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Residues in contact with LEU 208 (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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136A PHE* 3.8 28.5 - - + -
140A VAL* 4.1 21.1 - - + -
145A TRP* 4.4 6.1 - - - +
153A ILE* 3.8 20.2 - - + -
155A ASP 2.9 9.4 + - - +
156A VAL* 3.3 8.0 - - + +
157A ILE* 2.8 32.9 + - - +
207A ALA* 1.3 71.8 - - - +
209A PHE* 1.3 64.4 + - - +
210A ILE* 4.1 6.0 + - + -
244A LYS 4.3 7.2 - - - +
245A HIS* 3.7 23.6 - - - +
247A VAL* 4.2 17.3 - - + -
289A LEU* 4.5 11.9 - - + -
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Residues in contact with PHE 209 (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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157A ILE* 3.4 36.3 - - + +
159A ILE* 4.0 13.9 - - + -
195A LEU* 5.1 0.7 - - + -
199A LEU* 3.9 12.8 - - + -
202A LEU* 3.8 19.1 - - + -
207A ALA* 4.0 18.8 - - + -
208A LEU* 1.3 74.6 - - - +
210A ILE* 1.3 63.0 + - - +
211A ILE* 4.0 6.1 - - + -
228A ALA* 3.8 16.8 - - + -
231A TRP* 3.8 21.5 - + - -
232A PHE* 5.1 3.8 - + - -
245A HIS* 2.8 17.3 + - + -
246A PHE* 3.4 41.3 - + + -
247A VAL* 2.9 29.6 + - - +
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Residues in contact with ILE 210 (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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156A VAL* 3.5 31.9 - - + -
157A ILE 2.8 11.7 + - - +
158A ASN* 3.6 10.5 - - - +
159A ILE* 2.9 27.2 + - - +
208A LEU* 4.7 5.4 - - + -
209A PHE* 1.3 75.8 - - - +
211A ILE* 1.3 62.4 + - - +
212A ALA 3.6 0.3 + - - -
247A VAL* 3.6 16.2 - - + -
249A LEU* 3.6 43.1 - - + -
285A LEU* 4.3 4.0 - - + -
286A SER* 4.1 19.1 - - - +
289A LEU* 3.7 20.4 - - + -
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Residues in contact with ILE 211 (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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159A ILE* 3.8 24.0 - - + -
209A PHE* 4.2 3.6 - - + -
210A ILE* 1.3 75.6 - - - +
212A ALA* 1.3 61.2 + - - +
213A SER* 3.7 1.8 + - - -
216A PHE* 3.4 35.5 - - + -
221A THR* 4.0 15.7 - - + -
222A ILE* 4.4 3.8 - - + -
225A ALA* 3.5 34.5 - - + -
246A PHE* 4.1 25.8 - - + -
247A VAL 2.8 17.8 + - - +
248A ALA* 3.3 4.7 - - - +
249A LEU 2.9 24.5 + - - +
259A PHE* 4.8 1.1 - - + -
261A ILE* 4.6 3.8 - - + -
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Residues in contact with ALA 212 (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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158A ASN* 4.3 7.4 - - - +
159A ILE 2.8 16.9 + - - +
160A GLY* 3.7 10.6 - - - -
161A ILE 4.7 0.2 + - - -
164A SER* 3.5 41.5 + - - +
210A ILE 3.6 0.2 + - - -
211A ILE* 1.3 70.7 - - - +
213A SER* 1.3 63.7 + - - +
221A THR* 3.8 3.3 + - - +
249A LEU* 3.7 26.7 - - + -
283A ILE* 3.9 7.2 - - + -
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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