Contacts of the strand formed by residues 299 - 310 (chain B) in PDB entry 3D5K
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 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B GLU* 4.5 18.4 + - - +
297B PHE 3.5 3.3 + - - -
298B PRO* 1.3 72.7 - - - +
300B ILE* 1.3 63.0 + - - +
301B SER* 4.1 2.5 + - - -
329B SER 3.6 1.2 - - - +
330B ILE* 3.2 6.2 - - - -
331B ASN* 2.8 46.1 + - - +
333B PRO* 6.2 0.2 - - - -
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLU* 3.4 11.1 - - - +
126B LEU* 2.9 59.4 + - + +
128B LEU* 3.6 45.3 - - + -
129B PHE* 4.8 4.3 - - + -
298B PRO 4.0 4.4 + - - +
299B SER* 1.3 78.1 + - - +
301B SER* 1.3 66.2 + - - +
328B PRO* 6.1 2.7 - - + -
329B SER 3.4 7.0 - - - +
330B ILE* 4.2 23.3 - - + -
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ALA* 3.8 22.2 - - - +
124B TRP 3.3 9.0 - - - -
125B GLU* 5.2 2.5 - - - -
126B LEU* 5.0 0.6 - - - +
299B SER* 5.4 3.1 - - - -
300B ILE* 1.3 80.3 - - - +
302B LEU* 1.3 63.6 + - - +
303B THR* 5.0 1.2 + - - -
327B GLN 5.4 0.2 + - - -
328B PRO* 3.3 5.2 - - - +
329B SER* 2.8 47.6 + - - +
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 4.0 6.0 - - + +
123B ALA 3.3 2.1 + - - -
124B TRP* 2.9 65.9 + - + +
126B LEU* 4.4 14.1 - - + -
301B SER* 1.3 79.9 + - - +
303B THR* 1.3 80.3 + - - +
304B ALA* 4.0 12.1 - - + -
326B PHE* 3.7 36.8 - - + -
327B GLN 4.0 2.9 - - - +
328B PRO* 3.9 19.7 - - + -
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Residues in contact with THR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR 3.6 16.8 - - - +
122B THR* 4.1 15.8 - - + +
123B ALA* 3.2 18.6 + - - +
301B SER* 5.0 1.6 + - - -
302B LEU* 1.3 71.4 - - - +
304B ALA* 1.3 61.9 + - - +
305B ASN* 4.8 4.5 - - - +
325B LEU* 3.9 20.8 - - + +
326B PHE* 3.7 1.2 - - - -
327B GLN* 2.9 57.4 + - - +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY* 3.4 2.1 - - - -
121B THR* 2.9 44.3 + - + +
302B LEU* 4.0 21.5 - - + -
303B THR* 1.3 75.2 - - - +
305B ASN* 1.3 60.8 + - - +
325B LEU 3.3 10.5 - - - +
326B PHE* 4.4 10.3 - - + -
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Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B THR* 2.9 36.0 + - + +
119B LEU 3.5 15.5 - - - +
120B GLY* 4.1 3.8 - - - -
121B THR 4.9 1.9 + - - +
303B THR* 4.8 6.5 - - - +
304B ALA* 1.3 76.5 - - - +
306B ALA* 1.3 64.5 + - - +
323B SER* 5.1 0.9 + - - +
324B TRP* 3.4 7.4 - - - +
325B LEU* 3.0 61.2 + - - +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B THR* 3.1 5.6 - - - -
119B LEU* 2.9 34.1 + - - +
305B ASN* 1.3 79.5 - - - +
307B GLY* 1.3 57.0 + - - +
323B SER 3.4 10.1 - - - +
324B TRP* 4.4 6.5 - - + -
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Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL 3.6 10.3 - - - -
118B THR* 3.8 1.9 + - - -
305B ASN* 4.9 0.2 + - - -
306B ALA* 1.3 75.1 - - - +
308B THR* 1.3 68.5 + - - +
322B GLY* 3.4 6.9 - - - -
323B SER* 2.8 35.6 + - - +
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Residues in contact with THR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLY* 3.4 0.5 - - - -
117B VAL* 3.0 39.2 + - - +
118B THR* 5.2 0.6 - - - -
307B GLY* 1.3 79.1 - - - +
309B MET* 1.3 66.7 + - - +
316B LEU* 2.8 34.3 + - - +
317B PHE* 4.1 30.4 - - + -
318B ASP 5.3 0.2 - - - +
321B SER* 3.3 16.8 - - - +
322B GLY* 4.8 1.3 - - - -
323B SER* 3.6 1.9 + - - -
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Residues in contact with MET 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLN* 4.4 11.2 - - - +
98A ARG 4.2 3.6 - - - +
99A LEU* 3.7 27.6 - - + -
100A PRO* 3.2 24.1 - - + +
102A ASP* 4.4 0.5 - - - +
103A LEU* 3.6 13.7 - - + -
114B GLN* 4.3 17.5 - - - +
115B TYR 3.2 12.3 - - - +
116B GLY* 3.9 8.3 - - - -
118B THR* 6.5 0.4 - - - -
308B THR* 1.3 78.5 - - - +
310B SER* 1.3 64.2 + - - +
315B GLY 5.0 0.2 - - - -
316B LEU* 4.5 1.8 - - - -
321B SER* 3.0 19.0 + - - +
323B SER* 3.5 28.4 + - - +
324B TRP 5.5 1.8 - - - +
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Residues in contact with SER 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP* 3.3 16.9 + - - -
103A LEU* 3.8 7.3 - - - +
114B GLN* 3.4 1.9 - - - +
115B TYR* 2.7 40.6 + - - +
309B MET* 1.3 76.8 - - - +
311B ARG* 1.3 61.7 + - - +
312B GLN* 2.9 29.8 + - - +
315B GLY* 3.4 29.1 + - - -
316B LEU* 4.0 4.9 - - - +
321B SER* 5.3 0.4 - - - -
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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