Contacts of the strand formed by residues 303 - 315 (chain C) 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 PRO 303 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C PHE* 5.2 0.4 - - + -
53C LEU 3.2 19.7 - - - +
54C ASN* 3.3 17.9 - - - +
55C PRO* 3.3 6.7 - - + -
129C VAL* 3.3 4.7 - - - +
130C VAL* 3.0 47.0 + - + +
302C LEU* 1.3 96.8 - - + +
304C ARG* 1.3 60.3 + - - +
177D LEU* 3.6 8.3 - - + -
207D VAL* 3.2 26.0 - - - +
208D LEU* 4.1 11.0 - - + -
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Residues in contact with ARG 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C PHE* 3.0 4.9 - - - -
53C LEU 2.7 37.2 + - - -
127C THR* 2.9 41.0 + - - +
128C GLU* 3.4 8.2 - - - +
129C VAL* 3.7 13.4 - - + +
130C VAL* 5.9 0.2 - - - -
163C HIS* 4.5 9.1 - - - +
164C VAL 4.0 4.4 + - - -
165C PHE* 3.8 24.1 - - - +
282C CYS* 3.8 21.6 - - - +
284C ASP* 2.6 51.4 + - - +
302C LEU 4.1 0.4 + - - -
303C PRO* 1.3 74.8 - - - +
305C TYR* 1.3 60.0 + - - +
306C PHE* 3.1 28.4 - - + -
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Residues in contact with TYR 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLU* 2.7 37.7 + - + -
51C ALA 3.4 12.3 - - - -
52C PHE* 3.8 8.5 - + + +
126C LYS* 3.9 14.1 - - + +
127C THR* 2.4 37.7 + - - -
128C GLU* 2.8 23.2 + - + +
130C VAL* 5.6 4.0 - - + +
303C PRO 4.3 0.2 - - - -
304C ARG* 1.3 71.5 - - - +
306C PHE* 1.3 65.0 + - - +
307C LYS* 3.5 33.5 - - + +
231D PRO* 3.1 52.8 - - + +
232D ALA 3.9 5.7 + - - -
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Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE 3.6 0.2 - - - +
50C GLU* 3.1 6.4 - - - +
51C ALA 2.6 38.8 + - - +
52C PHE* 4.3 3.1 - - - -
53C LEU* 3.4 34.1 - - + -
125C VAL* 4.4 9.0 - - + -
126C LYS 3.3 6.7 - - - -
127C THR* 3.9 7.9 - - - -
165C PHE* 4.0 20.4 - + + -
166C ALA 4.5 3.8 - - - -
167C VAL* 4.8 0.7 - - + -
280C LEU* 3.9 31.4 - - + -
281C SER 4.4 2.0 - - - -
282C CYS* 3.9 8.5 - - + -
304C ARG* 3.1 46.2 - - + -
305C TYR* 1.3 80.8 - - - +
307C LYS* 1.3 61.9 + - - +
308C ILE* 3.8 15.9 - - + -
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Residues in contact with LYS 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLU* 3.3 40.3 + - + -
49C ILE 3.3 3.8 - - - +
50C GLU* 3.4 17.3 - - + -
124C SER 3.7 0.2 - - - +
125C VAL* 2.9 24.5 - - - +
126C LYS* 2.6 43.0 + - + +
260C THR* 5.5 1.1 - - + +
305C TYR* 3.5 22.0 - - + +
306C PHE* 1.3 75.1 - - - +
308C ILE* 1.3 64.6 + - - +
309C THR* 3.8 6.5 + - - +
233D LYS 4.5 16.3 + - - -
266D GLU* 4.8 11.3 + - - -
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Residues in contact with ILE 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLU* 3.4 3.8 - - - +
49C ILE* 2.8 49.7 + - + +
51C ALA* 5.3 1.8 - - + +
103C LEU* 6.0 0.4 - - + -
122C ALA* 3.8 16.4 - - + -
124C SER 3.5 8.3 - - - +
125C VAL* 3.6 14.6 - - + -
167C VAL* 4.6 3.8 - - + -
263C LEU* 4.7 2.9 - - + -
278C LEU* 4.1 17.9 - - + -
280C LEU* 4.0 24.0 - - + -
306C PHE* 3.8 21.8 - - + +
307C LYS* 1.3 77.7 - - - +
309C THR* 1.3 75.6 + - - +
310C LEU* 3.5 23.0 - - + +
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Residues in contact with THR 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C VAL* 4.3 12.6 - - + -
47C THR 3.5 3.1 - - - +
48C GLU* 3.7 31.8 - - + +
123C VAL* 2.7 38.4 + - - +
124C SER* 2.9 34.4 + - - +
125C VAL* 4.4 0.2 - - - -
260C THR* 5.0 3.6 - - - +
307C LYS* 3.8 8.8 + - - +
308C ILE* 1.3 76.5 - - - +
310C LEU* 1.3 55.7 + - - +
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C SER 4.4 0.5 - - - +
46C VAL* 3.5 6.5 - - - +
47C THR* 3.0 45.4 + - - +
49C ILE* 3.9 21.1 - - + -
105C LEU* 3.4 30.7 - - + -
120C TRP* 4.3 12.6 - - + -
121C GLU 3.1 11.2 - - - +
122C ALA* 4.2 3.8 - - + +
123C VAL* 4.5 1.6 - - - +
273C CYS* 4.4 10.8 - - - -
278C LEU* 3.8 20.4 - - + -
308C ILE* 3.5 27.1 - - + +
309C THR* 1.3 76.3 - - - +
311C ARG* 1.3 59.7 + - - +
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Residues in contact with ARG 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ASP* 5.8 4.0 - - - +
45C SER 4.6 7.0 - - - +
46C VAL* 5.1 8.3 - - + +
120C TRP* 3.4 6.1 - - - -
121C GLU* 2.7 65.0 + - + +
123C VAL* 4.0 15.1 - - + +
264C LEU* 3.7 19.3 - - - +
268C GLY 3.4 9.1 + - - -
269C VAL 3.9 0.2 + - - -
310C LEU* 1.3 74.3 - - - +
312C LYS* 1.3 72.7 + - - +
313C ARG* 2.6 39.0 - - - +
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Residues in contact with LYS 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C THR* 2.5 40.2 + - - +
42C GLY 2.6 28.6 + - - +
43C PRO* 3.3 32.6 + - + +
44C ASP* 5.6 0.4 - - - +
45C SER* 3.6 10.7 + - - +
108C LEU* 3.6 21.6 - - + +
118C GLN* 4.0 20.8 - - - +
119C MET 3.8 3.6 - - - -
120C TRP* 3.5 28.5 - - + -
311C ARG* 1.3 81.5 - - - +
313C ARG* 1.3 61.6 + - - +
314C TRP* 5.2 4.7 - - - -
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Residues in contact with ARG 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA* 3.3 29.1 - - - +
117C LEU 3.7 0.5 - - - +
118C GLN* 3.0 5.3 - - - -
119C MET* 2.7 45.4 + - + +
121C GLU* 3.0 31.4 + - + +
268C GLY 2.6 29.9 + - - -
269C VAL* 3.2 19.0 - - - +
272C LEU* 4.8 6.5 - - + +
311C ARG* 2.6 28.9 + - - +
312C LYS* 1.3 75.8 - - - +
314C TRP* 1.3 89.6 + - + +
315C VAL* 4.0 11.2 - - + +
360F VAL* 4.4 9.2 - - - -
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Residues in contact with TRP 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B CYS* 6.2 0.2 - - + -
20B PRO* 3.6 35.3 - - + +
21B ARG 5.2 0.9 - - - -
22B PRO* 3.0 31.5 - - + +
23B ALA 4.1 0.2 + - - -
43C PRO* 5.8 6.4 - - + +
109C ASN* 4.2 14.4 - - - -
111C ASP* 5.7 0.9 - - - -
116C THR* 3.3 31.0 - - + -
117C LEU* 3.2 25.6 - - - -
118C GLN* 3.1 49.4 + - + -
312C LYS 5.2 3.4 - - - -
313C ARG* 1.3 96.1 - - + +
315C VAL* 1.3 62.8 + - - +
360F VAL* 3.7 1.4 - - - +
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Residues in contact with VAL 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PRO* 3.5 8.7 - - - +
116C THR* 3.2 8.0 - - - -
117C LEU* 2.7 42.4 + - + +
119C MET* 3.5 26.2 - - + -
272C LEU* 4.7 7.9 - - + -
313C ARG* 4.0 15.7 - - + +
314C TRP* 1.3 80.7 - - - +
316C LYS* 1.3 74.2 + - - +
318C PRO* 4.7 1.3 - - + -
360F VAL* 3.2 22.0 - - + +
361F PRO 3.9 4.7 - - - +
362F GLY* 3.5 15.3 - - - -
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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