Contacts of the strand formed by residues 194 - 199 (chain K) 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 THR 194 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154K TRP* 3.7 5.9 - - - -
155K ASN* 2.7 49.1 + - - +
192K SER* 4.7 5.4 - - - -
193K ILE* 1.3 81.9 - - - +
195K CYS* 1.3 65.6 + - - +
196K ASN* 4.0 9.9 + - - +
207K ASP* 4.3 9.2 + - - +
208K LYS 4.2 0.2 - - - -
209K LYS* 3.7 44.9 - - + +
210K ILE* 4.4 0.7 - - - -
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Residues in contact with CYS 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121K VAL* 5.1 0.4 - - - -
140K CYS* 2.0 45.3 - - - -
152K LEU* 4.3 4.5 - - + -
153K LEU 3.7 4.9 - - - +
154K TRP* 3.4 29.2 - - + -
194K THR* 1.3 73.7 + - - +
196K ASN* 1.3 63.0 + - - +
197K VAL* 4.2 5.3 + - - +
206K VAL 3.9 0.2 - - - +
207K ASP* 3.3 5.2 - - - -
208K LYS* 3.1 47.4 + - - -
210K ILE* 4.4 2.5 - - - -
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Residues in contact with ASN 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151K THR 3.4 0.2 - - - +
152K LEU* 3.2 24.8 - - - -
153K LEU* 2.6 48.9 + - + +
155K ASN* 3.7 5.1 + - - +
156K SER* 3.3 32.8 + - - -
194K THR* 4.0 7.1 + - - +
195K CYS* 1.3 78.6 - - - +
197K VAL* 1.3 64.1 + - - +
206K VAL 3.4 3.6 - - - -
207K ASP* 3.2 29.2 + - - +
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Residues in contact with VAL 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119K PRO* 5.8 3.8 - - + -
121K VAL* 4.6 24.2 - - + -
140K CYS* 4.9 0.2 - - - -
142K VAL* 4.5 20.6 - - + -
150K VAL* 3.8 21.8 - - + -
151K THR 3.6 10.1 - - - +
152K LEU* 4.5 9.6 - - + -
153K LEU* 5.8 0.2 - - - -
195K CYS* 4.7 13.2 - - - +
196K ASN* 1.3 82.6 - - - +
198K ALA* 1.3 70.9 + - - +
204K THR* 5.3 1.8 - - + -
205K LYS* 3.3 5.9 - - - +
206K VAL* 2.6 46.3 + - + +
207K ASP* 5.3 0.2 - - - +
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Residues in contact with ALA 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119K PRO* 5.5 1.0 - - - +
150K VAL* 3.6 12.5 - - - +
151K THR* 3.2 40.8 + - - +
153K LEU* 6.3 1.1 - - + -
197K VAL* 1.3 80.8 - - - +
199K HIS* 1.3 60.9 + - - +
200K PRO* 3.9 5.8 - - + -
204K THR* 3.6 12.3 - - - +
205K LYS* 4.9 7.4 - - + -
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Residues in contact with HIS 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K THR 3.6 4.5 - - - -
119K PRO* 3.5 14.5 - - + +
145K TYR* 3.2 36.3 - - + -
146K PHE 3.2 24.3 + - - -
147K PRO 3.2 10.3 + - - -
148K GLU 5.3 0.2 - - - -
149K SER 3.4 19.1 - - - -
150K VAL* 3.4 11.9 - - + -
198K ALA* 1.3 74.2 - - - +
200K PRO* 1.3 71.9 - - - +
201K ALA* 3.0 12.2 + - + +
202K SER* 3.0 26.4 + - - +
203K SER* 3.2 15.1 + - - -
204K THR* 3.3 23.0 + - - +
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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