Contacts of the strand formed by residues 298 - 307 (chain A) in PDB entry 1SNG
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 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A LEU* 5.9 1.6 - - + -
156A ALA 3.8 0.6 + - - -
157A ILE* 3.5 24.1 - - + -
158A LEU 3.1 23.1 + - - +
266A GLN* 2.7 39.3 + - - +
268A VAL* 3.5 8.5 - - - +
280A PHE* 4.3 0.7 - - - -
296A VAL* 3.2 11.1 - - - +
297A ASP* 1.3 81.5 - - + +
299A VAL* 1.3 72.5 + - - +
300A ILE* 3.9 23.6 - - + +
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Residues in contact with VAL 299 (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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39A VAL* 6.0 2.5 - - + -
42A ALA* 5.3 6.3 - - + -
43A LEU* 5.2 6.5 - - + -
46A LEU* 4.5 12.6 - - + -
158A LEU* 3.4 28.3 - - + +
160A ASN* 6.2 0.7 - - + -
265A HIS 3.8 0.2 - - - +
266A GLN* 3.6 0.9 - - - -
267A LEU* 3.0 54.9 + - + +
268A VAL* 4.3 1.6 - - - +
271A LEU* 5.0 4.5 - - + -
280A PHE* 3.7 26.9 - - + -
296A VAL* 4.2 7.6 - - + -
298A THR* 1.3 84.8 + - - +
300A ILE* 1.3 66.6 + - - +
301A HIS* 4.2 1.8 - - + -
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Residues in contact with ILE 300 (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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144A LEU* 4.0 33.0 - - + +
145A LEU* 3.4 29.2 - - + -
146A PRO* 5.8 2.0 - - + -
149A ALA* 5.2 7.4 - - + -
157A ILE* 5.9 1.3 - - + -
158A LEU 2.9 9.4 + - - +
159A THR* 3.4 6.0 - - + -
160A ASN* 3.0 26.2 + - - +
264A PRO* 5.2 2.7 - - + -
265A HIS 3.3 12.8 - - - +
266A GLN* 4.3 16.2 - - + +
298A THR* 3.9 26.9 - - + +
299A VAL* 1.3 79.0 - - - +
301A HIS* 1.3 63.1 + - - +
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Residues in contact with HIS 301 (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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34A TRP* 3.8 21.9 - - + -
35A SER* 3.0 29.5 + - - -
38A SER* 3.5 19.8 - - - -
39A VAL* 4.0 13.4 - - + +
144A LEU* 4.3 2.5 - - - -
160A ASN* 2.6 37.5 + - + +
162A LEU 4.7 2.0 - - - -
263A GLN 3.8 0.5 - - - +
264A PRO* 3.7 0.5 - - - +
265A HIS* 2.8 40.0 + + + +
267A LEU* 4.0 21.1 - - + -
299A VAL* 5.2 2.2 - - + -
300A ILE* 1.3 75.7 - - - +
302A GLN* 1.3 76.9 + - - +
303A ALA* 3.9 5.3 - - + +
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Residues in contact with GLN 302 (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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141A ILE* 3.4 26.4 - - + +
143A GLU 5.0 0.5 - - - +
144A LEU* 3.4 26.4 - - + +
160A ASN 3.1 7.1 + - - -
161A ALA* 3.1 5.4 - - + -
162A LEU 3.0 22.3 + - - -
262A THR* 2.8 34.7 + - - +
263A GLN 3.6 11.2 - - - +
264A PRO* 3.5 28.4 - - + +
301A HIS* 1.3 81.3 - - - +
303A ALA* 1.3 59.2 + - - +
505A SO4 3.1 26.8 + - - -
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Residues in contact with ALA 303 (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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33A ILE* 3.9 6.4 + - + +
34A TRP* 3.8 36.3 - - - +
35A SER* 4.0 3.6 - - - +
141A ILE* 4.6 0.2 - - - -
162A LEU* 3.2 9.2 - - + +
261A LEU 3.9 1.1 - - - +
262A THR* 2.7 29.4 + - - -
263A GLN 3.7 6.1 + - - -
301A HIS* 3.9 9.3 + - + +
302A GLN* 1.3 74.4 - - - +
304A ARG* 1.3 56.8 + - - +
354A PHE* 3.9 16.4 - - + -
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Residues in contact with ARG 304 (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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139A GLY 4.9 1.2 + - - -
140A MET* 2.9 52.8 + - - +
141A ILE* 4.3 11.0 - - + +
162A LEU 2.8 9.4 + - - +
163A TRP* 3.3 26.2 - - + -
164A ALA 3.1 23.9 + - - -
260A GLU* 2.8 39.1 + - + +
261A LEU 3.5 4.7 - - - +
262A THR* 3.4 26.2 - - - +
303A ALA* 1.3 74.7 - - - +
305A LEU* 1.3 62.7 + - - +
354A PHE* 3.5 4.7 - - - -
505A SO4 5.3 1.6 + - - -
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Residues in contact with LEU 305 (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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33A ILE* 3.7 27.8 - - + -
163A TRP* 4.5 0.4 - - - -
164A ALA* 3.6 17.7 - - + +
166A ALA* 5.0 9.0 - - + +
219A LEU* 6.4 0.4 - - + -
259A PHE* 4.2 6.3 - - + +
260A GLU* 3.3 7.0 - - - +
261A LEU 3.1 30.7 + - - -
303A ALA 4.3 0.4 - - - -
304A ARG* 1.3 74.8 - - - +
306A ARG* 1.3 68.2 + - - +
307A VAL* 4.2 21.0 + - + -
344A ILE* 4.2 13.5 - - + -
346A VAL* 3.8 28.0 - - + -
354A PHE* 3.9 28.3 - - + -
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Residues in contact with ARG 306 (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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163A TRP* 3.8 16.1 - - + -
164A ALA 3.3 6.5 + - - -
165A LYS* 3.8 26.4 - - + +
166A ALA 3.7 21.5 + - - +
259A PHE 3.7 2.7 - - - -
260A GLU* 3.6 30.2 + - - +
305A LEU* 1.3 75.3 - - - +
307A VAL* 1.3 66.1 + - - +
308A ASP* 2.8 30.9 + - - +
364A PRO* 3.6 28.9 + - + +
365A GLY 3.2 26.7 + - - -
366A PRO 4.6 1.4 + - - -
367A ALA 3.2 27.8 + - - +
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Residues in contact with VAL 307 (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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166A ALA* 5.5 2.9 - - + +
168A TRP* 4.1 24.5 - - + -
194A MET* 4.0 19.1 - - + -
221A VAL* 6.4 0.2 - - + -
256A LEU* 4.1 9.4 - - + -
258A ARG* 3.5 4.3 - - - +
259A PHE* 2.7 75.6 + - + +
305A LEU* 4.2 12.8 - - + -
306A ARG* 1.3 76.4 - - - +
308A ASP* 1.3 62.7 + - - +
344A ILE* 4.0 15.3 - - + -
364A PRO* 4.7 0.2 - - - +
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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