Contacts of the strand formed by residues 304 - 316 (chain E) in PDB entry 1SID
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 ARG 304 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A LEU* 5.5 1.8 - - - -
52E PHE* 2.9 8.6 - - - +
53E LEU 2.7 38.9 + - - +
127E THR* 2.7 36.9 + - - +
128E GLU* 3.5 8.9 - - - +
129E VAL* 3.4 16.0 - - + +
130E VAL* 5.4 0.9 - - - -
163E HIS* 4.4 7.1 - - - +
164E VAL 4.2 10.3 + - - -
165E PHE* 3.8 26.8 - - - -
282E CYS* 3.9 13.5 - - - -
284E ASP* 2.5 45.9 + - - +
303E PRO* 1.3 76.2 - - - +
305E TYR* 1.3 60.6 + - - +
306E PHE* 3.2 27.0 - - + -
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Residues in contact with TYR 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PRO* 3.0 55.4 - - + +
232A ALA 2.8 10.8 + - - -
233A LYS 4.4 0.9 + - - -
50E GLU* 2.7 38.7 - - + +
51E ALA 3.4 10.5 - - - -
52E PHE* 4.0 4.7 - - + -
126E LYS* 3.9 10.8 - - + -
127E THR* 2.5 37.6 + - - -
128E GLU* 3.0 21.6 + - + +
130E VAL* 5.2 2.4 - - + +
304E ARG* 1.3 69.1 - - - +
306E PHE* 1.3 78.6 + - - +
307E LYS* 3.2 34.3 - - + +
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Residues in contact with PHE 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE 3.2 1.9 - - - +
50E GLU* 3.0 3.8 - - - -
51E ALA* 2.7 41.8 + - + +
52E PHE* 4.2 3.8 - - - -
53E LEU* 3.8 26.2 - - + -
125E VAL* 4.6 4.3 - - + -
126E LYS 3.5 4.3 - - - -
127E THR* 4.2 3.8 - - - -
165E PHE* 4.2 19.3 - + + -
166E ALA 4.5 1.6 - - - -
167E VAL* 4.4 9.4 - - + -
280E LEU* 3.7 36.6 - - + -
281E SER 4.4 0.7 - - - -
282E CYS* 4.0 8.1 - - + -
304E ARG* 3.2 48.5 - - + -
305E TYR* 1.3 98.8 - - - +
307E LYS* 1.3 59.6 + - - +
308E ILE* 3.3 19.5 - - + -
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Residues in contact with LYS 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LYS 4.3 8.8 + - - -
266A GLU* 4.3 16.8 + - - -
48E GLU* 3.2 47.1 + - + -
49E ILE 3.3 4.9 - - - +
50E GLU* 3.8 19.5 - - + -
125E VAL* 2.9 24.9 - - - -
126E LYS* 2.7 39.4 + - + +
260E THR* 6.3 0.4 - - + -
305E TYR* 3.2 28.5 - - + +
306E PHE* 1.3 72.7 - - - +
308E ILE* 1.3 62.8 + - - +
309E THR* 3.7 6.8 + - - +
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Residues in contact with ILE 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E THR 3.6 1.9 - - - +
48E GLU* 3.4 2.5 - - - -
49E ILE* 2.8 43.0 + - + +
51E ALA* 6.0 0.4 - - + -
122E ALA* 4.0 14.6 - - + -
124E SER 3.7 5.2 - - - +
125E VAL* 3.8 15.3 - - + -
167E VAL* 4.5 5.8 - - + -
263E LEU* 4.9 0.2 - - + -
278E LEU* 4.3 10.8 - - + -
280E LEU* 4.0 26.9 - - + -
306E PHE* 3.3 37.2 - - + +
307E LYS* 1.3 75.6 - - - +
309E THR* 1.3 66.1 + - - +
310E LEU* 3.2 31.1 - - + +
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Residues in contact with THR 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E VAL* 4.7 12.1 - - + -
47E THR 3.3 4.5 - - - +
48E GLU* 3.8 28.0 - - + +
122E ALA* 3.8 0.9 - - - -
123E VAL* 2.9 27.3 + - - +
124E SER* 3.0 35.2 + - - +
125E VAL* 4.2 0.5 + - - -
260E THR* 4.8 4.5 - - - +
307E LYS* 3.8 9.2 + - - +
308E ILE* 1.3 73.9 - - - +
310E LEU* 1.3 63.0 + - - +
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Residues in contact with LEU 310 (chain E).
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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46E VAL* 3.4 5.3 - - - +
47E THR* 2.8 53.0 + - + +
49E ILE* 4.7 7.2 - - + -
105E LEU* 3.8 24.7 - - + -
120E TRP* 3.6 29.1 - - + -
121E GLU 2.9 20.0 - - - +
122E ALA* 3.4 11.9 - - + +
123E VAL* 4.4 2.7 - - - +
273E CYS* 5.4 2.9 - - - -
278E LEU* 4.4 12.6 - - + -
308E ILE* 3.2 29.8 - - + +
309E THR* 1.3 76.0 - - - +
311E ARG* 1.3 57.8 + - - +
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Residues in contact with ARG 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ASP* 6.1 1.8 - - - -
45E SER 4.2 12.1 - - - +
46E VAL* 5.0 6.1 - - + -
119E MET 3.5 1.7 - - - +
120E TRP* 3.5 11.8 - - - -
121E GLU* 2.6 76.1 + - + +
123E VAL* 3.8 18.2 - - + +
264E LEU* 3.7 16.9 - - - +
268E GLY 3.4 16.8 + - - -
310E LEU* 1.3 73.6 - - - +
312E LYS* 1.3 65.9 + - - +
313E ARG* 3.2 27.5 + - - +
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Residues in contact with LYS 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E THR* 3.1 27.1 + - - +
42E GLY 2.6 24.3 + - - +
43E PRO 3.0 28.1 - - - +
44E ASP* 5.1 3.7 - - - +
45E SER* 3.3 26.1 + - - +
108E LEU* 4.3 18.5 - - + +
118E GLN* 4.0 25.4 - - + +
119E MET 3.8 4.5 - - - -
120E TRP* 3.8 26.9 - - + -
311E ARG* 1.3 78.4 - - - +
313E ARG* 1.3 61.3 + - - +
314E TRP* 4.0 5.2 + - - -
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Residues in contact with ARG 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ALA* 4.1 25.3 - - - +
117E LEU 3.4 0.2 - - - +
118E GLN* 3.1 6.5 - - - -
119E MET 2.9 43.7 + - - +
121E GLU* 3.0 45.2 + - + +
267E ASN 4.6 1.8 + - - -
268E GLY 2.6 26.9 + - - -
269E VAL* 3.3 24.9 + - - +
272E LEU* 4.5 12.1 - - + -
311E ARG* 3.2 15.1 + - - +
312E LYS* 1.3 73.0 - - - +
314E TRP* 1.3 78.4 + - - +
315E VAL* 3.4 4.7 - - + +
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Residues in contact with TRP 314 (chain E).
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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20D PRO* 4.0 28.4 - - + +
21D ARG 5.1 0.7 - - - +
22D PRO* 3.3 32.6 - - + +
109E ASN* 3.3 19.1 - - - -
112E LEU* 3.9 22.7 - - + -
116E THR* 3.2 26.2 - - - +
117E LEU 2.8 31.0 - - - -
118E GLN* 3.1 45.6 + - + -
312E LYS 4.0 4.9 + - - -
313E ARG* 1.3 92.0 + - - +
315E VAL* 1.3 59.4 + - - +
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Residues in contact with VAL 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D PRO* 3.1 19.9 - - - +
115E ASP 3.2 1.2 - - - +
116E THR* 3.4 2.9 - - - -
117E LEU* 2.5 45.6 + - + +
119E MET* 3.7 38.8 - - + -
272E LEU* 4.8 15.3 - - + -
313E ARG* 3.4 11.4 - - + +
314E TRP* 1.3 77.6 - - - +
316E LYS* 1.3 74.1 + - - +
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Residues in contact with LYS 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D PRO* 4.3 14.3 - - + +
114E CYS* 3.1 24.2 + - - +
115E ASP* 3.0 21.4 + - + +
117E LEU* 4.7 1.3 - - - -
119E MET* 5.9 0.3 - - - +
315E VAL* 1.3 89.4 - - - +
317E ASN* 1.3 86.2 + - - +
318E PRO* 3.2 12.8 - - + +
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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