Contacts of the strand formed by residues 201 - 209 (chain M) in PDB entry 3QUM
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 SER 201 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197M THR* 3.7 5.9 - - - +
198M HIS* 2.7 29.1 + - - +
199M LYS 3.8 3.0 - - - +
200M THR* 1.3 76.5 + - - +
202M THR* 1.3 60.4 + - - +
203M SER* 2.4 51.0 + - - +
204M PRO 5.2 0.5 - - - -
205M ILE* 4.8 17.8 - - - +
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Residues in contact with THR 202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197M THR* 4.7 5.3 - - - +
199M LYS 4.3 2.5 + - - -
200M THR 4.1 2.0 + - - +
201M SER* 1.3 72.6 - - - +
203M SER* 1.3 64.7 + - - +
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Residues in contact with SER 203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197M THR* 3.3 10.5 - - - +
201M SER* 2.4 41.5 + - - +
202M THR* 1.3 83.2 + - - +
204M PRO* 1.3 75.3 - - - +
205M ILE* 4.1 0.5 + - - +
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Residues in contact with PRO 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195M GLU* 4.1 25.4 - - + +
196M ALA 4.1 0.4 - - - +
197M THR* 3.4 22.2 - - + +
201M SER* 5.2 0.4 - - - -
203M SER* 1.3 93.3 - - - +
205M ILE* 1.3 62.5 + - - +
206M VAL* 3.9 10.8 + - + +
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Residues in contact with ILE 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112M ALA* 5.9 2.5 - - + -
113M PRO* 4.7 28.7 - - + +
115M VAL* 4.2 27.3 - - + +
194M CYS 3.8 0.5 - - - +
195M GLU* 3.2 4.7 - - - -
196M ALA* 2.6 59.9 + - + +
197M THR* 5.0 2.5 - - - -
198M HIS* 5.7 2.2 - - + +
201M SER* 4.8 15.7 - - - -
203M SER 5.0 2.2 - - - +
204M PRO* 1.3 75.4 - - + +
206M VAL* 1.3 61.5 + - - +
207M LYS* 4.3 6.5 - - + +
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Residues in contact with VAL 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193M THR* 4.1 15.7 - - + +
194M CYS 3.4 3.1 - - - -
195M GLU* 3.7 27.8 - - + +
204M PRO* 3.9 15.4 + - + +
205M ILE* 1.3 82.4 - - - +
207M LYS* 1.3 70.5 + - - +
208M SER* 5.3 2.7 - - - +
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Residues in contact with LYS 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115M VAL* 3.2 53.9 - - + +
116M SER* 4.6 4.7 - - - -
117M ILE* 4.1 19.4 - - + +
193M THR* 3.5 1.5 - - - -
194M CYS* 2.9 36.2 + - + +
205M ILE* 5.4 5.6 - - + +
206M VAL* 1.3 80.3 + - - +
208M SER* 1.3 62.9 + - - +
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Residues in contact with SER 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M ILE* 4.4 9.0 - - - +
191M SER* 5.3 2.0 + - - -
192M TYR 2.8 24.7 - - - -
193M THR* 3.1 26.3 - - - +
206M VAL* 5.3 3.5 - - - +
207M LYS* 1.3 70.0 - - - +
209M PHE* 1.3 66.6 + - - +
210M ASN* 5.7 0.7 + - - -
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Residues in contact with PHE 209 (chain M).
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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127K VAL* 4.6 26.2 - - + -
117M ILE* 4.5 21.3 - - + -
118M PHE 4.5 4.5 - - - -
119M PRO* 3.9 37.7 - - + -
120M PRO* 5.0 0.4 - - + -
132M VAL* 4.3 13.9 - - + -
186M TYR* 3.9 22.0 - + - -
190M ASN 3.9 1.6 - - - +
191M SER* 3.7 0.5 - - - -
192M TYR* 3.4 50.3 + + + +
208M SER* 1.3 82.3 - - - +
210M ASN* 1.3 87.6 + - - +
212M ASN* 5.4 2.2 - - - +
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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