Contacts of the strand formed by residues 180 - 192 (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 THR 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A MET* 6.2 0.3 - - - +
170A LYS 3.8 0.3 - - - +
171A THR* 3.5 3.5 - - - +
172A VAL* 2.9 47.3 + - + +
178A LYS 3.5 4.9 + - - -
179A GLU* 1.3 74.3 - - - +
181A ILE* 1.3 74.4 + - - +
182A SER* 5.6 2.9 - - - -
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Residues in contact with ILE 181 (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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169A TYR* 4.0 20.4 - - + -
170A LYS 3.4 7.6 - - - +
171A THR* 4.2 22.9 - - + +
179A GLU* 4.3 11.2 + - + +
180A THR* 1.3 87.0 - - - +
182A SER* 1.3 65.7 + - - +
183A HIS* 3.9 24.7 - - + +
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Residues in contact with SER 182 (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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169A TYR* 3.1 5.2 - - - +
170A LYS* 2.8 40.5 + - - +
172A VAL* 5.8 1.9 - - - +
180A THR* 4.4 3.8 - - - -
181A ILE* 1.3 74.8 - - - +
183A HIS* 1.3 69.2 + - - +
184A TRP* 2.7 31.7 + - - -
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Residues in contact with HIS 183 (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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154A LYS* 3.2 29.7 + - - +
168A TYR 3.6 2.9 - - - -
169A TYR* 3.6 25.0 - + + +
181A ILE* 3.9 14.5 - - + +
182A SER* 1.3 82.6 - - - +
184A TRP* 1.3 68.1 + - - +
218A PRO* 3.4 7.1 - - - +
219A GLU* 3.1 31.4 + - + -
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Residues in contact with TRP 184 (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* 6.0 0.4 - - - -
144A TYR* 5.5 2.0 - - - -
167A ARG* 3.3 3.5 - - - -
168A TYR* 2.9 68.6 + + + +
170A LYS* 3.6 23.9 - - + +
182A SER* 2.7 38.5 + - - -
183A HIS* 1.3 91.7 - - - +
185A VAL* 1.3 62.2 + - - +
216A SER* 3.9 18.8 - - - -
217A ASP* 3.3 28.0 - - - -
218A PRO* 3.4 27.6 - - + -
219A GLU* 3.9 9.9 + - - +
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Residues in contact with VAL 185 (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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165A GLN* 3.6 40.8 - - + +
166A VAL 3.4 4.0 - - - -
167A ARG* 4.0 11.0 - - + -
184A TRP* 1.3 74.9 - - - +
186A SER* 1.3 66.4 + - - +
187A ILE* 4.3 10.2 - - + +
215A ARG* 5.9 0.2 - - - +
216A SER* 3.4 1.4 - - - -
217A ASP* 3.0 46.6 + - + +
218A PRO 4.5 8.5 - - - +
219A GLU* 4.7 12.8 - - + +
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Residues in contact with SER 186 (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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98A VAL* 4.4 5.6 - - - -
164A ILE 3.7 0.7 - - - +
165A GLN* 3.4 4.3 - - - +
166A VAL 2.8 38.5 + - - -
168A TYR* 3.3 11.8 - - - -
185A VAL* 1.3 71.7 - - - +
187A ILE* 1.3 62.8 + - - +
188A LEU* 3.8 6.0 - - - +
214A TYR* 2.9 32.6 + - - -
215A ARG 3.1 12.8 - - - -
216A SER* 3.0 16.6 + - - -
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Residues in contact with ILE 187 (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* 4.1 17.0 - - + -
163A LEU* 3.4 31.4 - - + -
164A ILE 3.4 6.1 - - - +
165A GLN* 4.0 26.5 - - + -
185A VAL* 4.3 9.2 - - + +
186A SER* 1.3 74.7 - - - +
188A LEU* 1.3 65.3 + - - +
214A TYR* 3.4 5.9 - - - -
215A ARG* 3.2 50.9 + - + +
217A ASP* 5.6 1.6 - - - +
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Residues in contact with LEU 188 (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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94A ALA* 4.0 31.2 - - + -
97A TYR* 4.2 11.0 - - + -
98A VAL* 4.2 3.6 - - + -
162A ASP 3.6 0.9 - - - +
163A LEU* 3.4 8.5 - - - -
164A ILE* 2.9 42.6 + - + +
166A VAL* 4.1 14.1 - - + -
186A SER* 3.8 14.8 - - - +
187A ILE* 1.3 81.2 - - - +
189A ASN* 1.3 60.7 + - - +
190A PHE* 3.8 3.6 + - + -
209A PHE* 4.9 3.4 - - + -
211A VAL* 4.1 24.0 - - + -
213A GLU 3.5 4.9 - - - +
214A TYR* 3.8 26.9 - - + -
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Residues in contact with ASN 189 (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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162A ASP* 3.1 34.1 + - - +
163A LEU* 4.2 14.5 - - + +
188A LEU* 1.3 71.6 - - - +
190A PHE* 1.3 61.4 + - - +
211A VAL* 3.3 5.5 - - - -
212A SER* 2.8 43.4 + - - +
213A GLU* 2.9 36.2 + - + +
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Residues in contact with PHE 190 (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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90A THR* 3.6 24.5 - - + -
158A PHE* 4.1 7.4 - + - -
161A LYS 3.5 16.6 - - - -
162A ASP* 3.0 51.8 + - - +
163A LEU 3.8 0.4 - - - -
164A ILE* 3.4 33.9 - - + -
188A LEU* 4.3 4.5 - - + +
189A ASN* 1.3 79.7 + - - +
191A SER* 1.3 72.3 + - - +
192A TYR* 4.1 14.8 - + - -
209A PHE* 3.9 29.4 - + + -
210A GLN 3.2 11.4 - - - +
211A VAL* 4.7 4.0 - - + -
212A SER* 4.7 0.9 - - - +
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Residues in contact with SER 191 (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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190A PHE* 1.3 84.4 - - - +
192A TYR* 1.3 71.3 + - - +
193A VAL* 4.7 7.1 - - - +
208A GLY 3.7 0.3 - - - +
209A PHE* 3.8 3.3 - - - -
210A GLN* 3.1 38.2 + - - +
212A SER* 5.2 6.4 + - - -
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Residues in contact with TYR 192 (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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85A TYR* 3.6 42.8 - + + -
89A ILE* 3.8 7.4 + - - +
90A THR* 2.4 43.4 + - - +
93A PHE* 5.1 2.7 - + - -
190A PHE* 4.1 19.7 - + - -
191A SER* 1.3 78.8 - - - +
193A VAL* 1.3 62.1 + - - +
194A ASN 4.0 0.9 + - - -
207A LEU* 3.3 40.4 - - + +
208A GLY 3.2 4.7 - - - -
209A PHE* 3.8 28.7 - + + -
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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