Contacts of the strand formed by residues 209 - 218 (chain A) in PDB entry 4MEI
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 PHE 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A THR* 4.3 10.8 - - + -
93A PHE* 3.9 33.4 - - + -
94A ALA* 3.9 22.2 - - + -
97A TYR* 4.7 2.2 - - + -
119A LEU* 3.5 28.1 - - + -
164A ILE* 5.1 1.1 - - + -
188A LEU* 4.9 2.2 - - + -
190A PHE* 3.9 34.1 - + + -
191A SER 3.8 4.0 - - - -
192A TYR* 3.8 33.2 - + + -
205A ASN* 2.8 33.1 + - - +
207A LEU* 3.3 3.2 - - + -
208A GLY* 1.3 77.2 - - - +
210A GLN* 1.3 67.8 + - - +
211A VAL* 3.7 23.6 - - + -
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Residues in contact with GLN 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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118A LEU 3.1 26.1 + - - -
119A LEU 3.3 4.3 - - - -
120A SER 3.3 14.3 + - - -
121A SER* 3.3 25.4 - - - +
122A PRO* 4.0 8.3 - - - +
190A PHE* 3.2 5.5 - - - -
191A SER* 3.1 43.1 + - - +
193A VAL* 3.8 28.7 - - + +
205A ASN* 4.5 1.4 - - - +
208A GLY* 3.5 11.4 - - - +
209A PHE* 1.3 83.4 + - - +
211A VAL* 1.3 64.0 + - - +
212A SER* 3.6 2.2 + - - -
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Residues in contact with VAL 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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97A TYR* 3.8 41.5 - - + +
119A LEU 2.7 20.4 + - - +
120A SER* 3.5 0.2 - - - -
121A SER* 3.1 19.8 + - - -
124A GLU* 3.3 12.9 - - + +
188A LEU* 4.1 16.2 - - + -
189A ASN 3.3 7.2 - - - +
190A PHE* 4.8 1.1 - - + -
209A PHE* 3.7 24.9 - - + -
210A GLN* 1.3 70.0 - - - +
212A SER* 1.3 58.1 - - - +
213A GLU 3.3 27.1 - - - +
214A TYR* 4.1 5.8 - - + -
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Residues in contact with SER 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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121A SER* 3.4 16.7 + - - -
124A GLU* 3.7 4.0 - - - +
127A ARG* 3.0 22.7 + - - -
189A ASN* 2.8 36.8 + - - +
190A PHE* 4.4 1.2 + - - -
191A SER* 5.2 5.6 + - - -
210A GLN* 3.6 4.4 + - - -
211A VAL* 1.3 73.0 - - - +
213A GLU* 1.3 64.0 + - - +
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Residues in contact with GLU 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLU* 3.9 5.4 - - - -
127A ARG* 4.4 10.2 + - - -
187A ILE 4.5 0.7 - - - -
188A LEU* 3.5 0.9 - - - -
189A ASN* 2.9 47.3 + - + +
211A VAL* 3.3 11.2 - - - +
212A SER* 1.3 89.1 + - - +
214A TYR* 1.3 61.7 + - - +
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Residues in contact with TYR 214 (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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97A TYR* 3.8 23.8 - + - -
98A VAL* 4.0 6.0 - - + +
101A ARG* 3.4 37.7 + - - +
102A GLU* 2.6 40.2 + - - +
124A GLU* 3.8 21.7 + - - +
186A SER* 2.9 34.6 + - - -
187A ILE 3.4 7.2 - - - -
188A LEU* 3.8 22.0 - - + -
211A VAL* 4.1 4.5 - - + -
213A GLU* 1.3 78.1 - - - +
215A ARG* 1.3 75.4 + - - +
216A SER* 4.1 1.1 - - - -
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Residues in contact with ARG 215 (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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186A SER* 3.1 27.6 - - - -
187A ILE* 3.2 34.7 + - + +
214A TYR* 1.3 85.6 - - - +
216A SER* 1.3 60.2 + - - +
217A ASP* 2.9 35.5 + - - +
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Residues in contact with SER 216 (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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102A GLU* 3.5 20.5 - - - -
168A TYR* 2.6 28.6 + - - -
184A TRP* 3.9 14.4 - - - -
185A VAL 3.4 7.0 + - - -
186A SER* 3.0 10.7 + - - -
214A TYR* 4.1 1.7 - - - -
215A ARG* 1.3 78.4 - - - +
217A ASP* 1.3 69.7 + - - +
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Residues in contact with ASP 217 (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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184A TRP* 3.3 7.2 - - - -
185A VAL* 3.0 41.4 + - + +
187A ILE* 5.6 2.3 - - - +
215A ARG* 2.9 47.6 + - - +
216A SER* 1.3 81.5 + - - +
218A PRO* 1.3 78.4 - - + +
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Residues in contact with PRO 218 (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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183A HIS 3.4 14.1 - - - +
184A TRP* 3.4 24.9 - - + -
185A VAL* 4.5 4.8 - - - +
217A ASP* 1.3 96.2 - - + +
219A GLU* 1.3 65.2 + - - +
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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