Contacts of the strand formed by residues 249 - 256 (chain P) in PDB entry 3Q2K
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 GLU 249 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253O THR* 5.4 1.0 + - - -
262O ARG* 5.1 11.0 + - - -
159P ASN* 3.9 16.5 + - + -
160P VAL* 3.5 0.9 - - - -
161P PHE* 2.7 58.5 + - + -
162P TRP* 3.5 6.7 - - - -
247P ASN 3.7 1.6 - - - -
248P LEU* 1.3 93.7 - - + +
250P GLY* 1.3 62.7 + - - +
251P SER* 2.7 31.4 + - - +
262P ARG* 3.3 19.6 + - - -
264P GLY* 5.5 0.3 - - - -
265P GLY 3.4 12.8 - - - +
266P VAL* 4.0 8.6 - - - +
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Residues in contact with GLY 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159P ASN 3.2 7.4 - - - -
160P VAL* 4.5 0.9 - - - -
162P TRP* 4.3 3.1 - - - -
192P TYR* 4.1 13.5 - - - -
249P GLU* 1.3 74.1 - - - +
251P SER* 1.3 61.1 + - - -
264P GLY 3.9 1.6 - - - +
265P GLY 2.9 14.0 + - - +
266P VAL 3.5 13.3 + - - -
268P VAL* 2.8 32.3 + - - -
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Residues in contact with SER 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157P THR 4.3 1.1 + - - -
158P VAL* 3.0 10.7 - - - +
159P ASN* 2.8 46.7 + - - +
192P TYR* 4.4 1.0 - - - -
249P GLU* 2.7 29.7 + - - -
250P GLY* 1.3 75.6 - - - +
252P ILE* 1.3 61.4 + - - +
253P THR* 5.3 1.8 + - - -
262P ARG* 4.5 8.7 + - - -
263P VAL 2.9 19.1 - - - -
264P GLY* 3.9 7.9 - - - -
268P VAL* 3.8 6.0 - - - +
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Residues in contact with ILE 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138P LEU* 4.8 4.9 - - + -
141P VAL* 5.4 2.7 - - + -
156P VAL* 4.5 7.0 - - + -
157P THR 3.3 3.1 - - - +
158P VAL* 3.6 25.1 - - + -
195P LEU* 4.0 24.7 - - + +
196P LEU* 5.5 0.9 - - + +
199P LEU* 3.8 26.5 - - + -
200P VAL* 5.2 1.6 - - + -
251P SER* 1.3 75.1 - - - +
253P THR* 1.3 65.1 + - - +
254P ILE* 4.1 23.5 - - + +
261P VAL* 4.1 1.6 - - + +
262P ARG* 3.5 1.7 - - - -
263P VAL* 3.0 55.0 + - + +
268P VAL* 4.0 7.8 - - + +
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Residues in contact with THR 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O ASN* 5.7 1.0 + - - -
161O PHE* 4.1 18.4 - - + -
248O LEU* 5.1 3.1 - - + -
249O GLU* 5.5 0.4 + - - +
155P MET* 3.8 0.4 - - + +
156P VAL* 3.2 7.1 - - - +
157P THR* 2.7 44.9 + - - +
251P SER* 5.3 2.3 + - - -
252P ILE* 1.3 74.1 - - - +
254P ILE* 1.3 66.8 + - - +
255P LEU* 4.0 26.2 - - + -
260P THR* 6.0 0.2 - - + -
261P VAL 3.4 10.8 - - - +
262P ARG* 2.9 36.4 + - + +
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Residues in contact with ILE 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141P VAL* 3.9 27.4 - - + -
145P ILE* 4.0 14.6 - - + -
150P PHE* 3.5 32.8 - - + -
153P ILE* 4.1 24.0 - - + -
155P MET 3.6 3.1 - - - +
156P VAL* 4.5 7.2 - - + -
199P LEU* 4.8 1.3 - - + -
200P VAL* 4.1 14.1 - - + -
252P ILE* 4.1 23.8 - - + -
253P THR* 1.3 80.1 - - - +
255P LEU* 1.3 64.0 + - - +
260P THR* 3.5 0.7 - - - -
261P VAL* 2.9 38.6 + - + +
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Residues in contact with LEU 255 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161O PHE* 3.5 45.3 - - + -
240O THR* 4.1 13.0 - - + -
242O LEU 6.3 0.2 - - - -
243O THR* 4.2 12.8 - - + +
248O LEU* 3.7 14.6 - - + -
153P ILE* 3.9 1.9 - - - +
154P TYR* 2.9 25.7 + - + +
155P MET* 2.8 33.3 + - + +
253P THR* 4.0 11.9 - - + -
254P ILE* 1.3 79.7 - - - +
256P GLY* 1.3 59.4 - - - +
259P GLY 3.8 2.2 - - - +
260P THR* 3.5 35.4 - - + +
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Residues in contact with GLY 256 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242O LEU 4.1 5.9 - - - +
244O TYR* 3.7 9.7 + - - +
150P PHE* 3.9 12.2 - - - -
152P ARG 3.1 14.1 - - - -
153P ILE* 4.0 4.3 - - - -
154P TYR* 3.7 8.1 - - - -
255P LEU* 1.3 74.9 - - - +
257P GLU* 1.3 67.4 + - - +
258P LYS 3.2 2.9 - - - -
259P GLY 2.9 20.2 + - - +
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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