Contacts of the strand formed by residues 303 - 316 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D LEU 3.3 7.6 - - - +
54D ASN* 3.4 9.6 - - - +
55D PRO* 3.2 25.8 - - + -
129D VAL* 3.3 5.4 - - - +
130D VAL* 3.1 56.7 + - + +
302D LEU* 1.3 92.9 - - + +
304D ARG* 1.3 61.1 + - - +
177E LEU* 3.9 3.6 - - + -
207E VAL* 3.3 23.3 - - - +
208E LEU* 4.0 9.4 - - + -
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Residues in contact with ARG 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D PHE* 2.9 30.7 - - - +
53D LEU 3.0 14.5 + - - +
127D THR* 2.7 43.9 + - - +
128D GLU* 3.2 6.2 - - - +
129D VAL* 3.4 19.2 - - + +
130D VAL* 5.5 1.6 - - - -
163D HIS* 4.7 6.9 - - - +
164D VAL 4.2 10.7 + - - -
165D PHE* 4.1 19.5 - - - +
282D CYS* 3.9 14.6 - - - +
284D ASP* 2.6 43.3 + - - +
303D PRO* 1.3 76.7 - - - +
305D TYR* 1.3 59.2 + - - +
306D PHE* 3.3 30.7 - - + -
208E LEU* 6.1 0.7 - - - -
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Residues in contact with TYR 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLU* 2.9 49.8 + - + +
51D ALA* 3.3 12.1 - - - -
52D PHE* 4.1 4.9 - + + -
126D LYS* 4.4 13.0 - - + -
127D THR* 2.5 36.7 + - - -
128D GLU* 2.8 22.0 + - + +
130D VAL* 5.3 3.6 - - + +
304D ARG* 1.3 68.9 - - - +
306D PHE* 1.3 80.0 + - - +
307D LYS* 3.9 20.2 - - + +
231E PRO* 3.2 51.6 - - + -
232E ALA 3.5 6.2 + - - -
233E LYS* 3.3 9.4 - - - -
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Residues in contact with PHE 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE 3.4 0.2 - - - +
50D GLU* 3.0 7.1 - - - +
51D ALA 2.7 41.0 + - - +
52D PHE* 3.8 4.7 - - - -
53D LEU* 3.8 32.8 - - + -
125D VAL* 4.5 9.4 - - + -
126D LYS 3.3 5.8 - - - -
127D THR* 4.2 4.3 - - - -
165D PHE* 4.4 15.0 - + - -
166D ALA 4.9 0.4 - - - -
167D VAL* 5.0 0.2 - - + -
280D LEU* 3.5 36.6 - - + -
281D SER 4.6 3.4 - - - -
282D CYS* 4.2 4.5 - - + -
304D ARG* 3.3 48.0 - - + -
305D TYR* 1.3 92.4 - - - +
307D LYS* 1.3 61.1 + - - +
308D ILE* 3.3 18.2 - - + -
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Residues in contact with LYS 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D GLU* 3.3 41.6 + - + -
49D ILE 3.3 5.6 - - - +
50D GLU* 3.9 24.9 + - + +
125D VAL* 3.0 23.5 - - - -
126D LYS* 2.8 42.0 + - + +
305D TYR* 3.9 18.4 - - + +
306D PHE* 1.3 75.3 - - - +
308D ILE* 1.3 63.4 + - - +
309D THR* 3.6 8.4 + - - +
233E LYS 4.7 4.6 + - - -
266E GLU* 4.6 15.6 + - - -
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Residues in contact with ILE 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D THR 3.6 1.4 - - - +
48D GLU* 3.4 4.7 - - - +
49D ILE* 2.8 42.6 + - + +
51D ALA* 5.6 1.1 - - + +
103D LEU* 6.3 0.2 - - + -
122D ALA* 4.2 13.0 - - + -
124D SER 3.9 7.4 - - - +
125D VAL* 3.7 12.8 - - + -
167D VAL* 4.6 4.9 - - + -
263D LEU* 4.8 1.6 - - + -
278D LEU* 3.9 19.1 - - + -
280D LEU* 3.8 23.8 - - + -
306D PHE* 3.3 32.5 - - + -
307D LYS* 1.3 74.2 - - - +
309D THR* 1.3 67.8 + - - +
310D LEU* 3.6 28.6 - - + +
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Residues in contact with THR 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D VAL* 4.2 16.6 - - + -
47D THR 3.5 1.8 - - - -
48D GLU* 3.8 28.0 - - + +
122D ALA* 3.9 0.7 - - - -
123D VAL* 2.8 32.3 + - + +
124D SER* 2.9 30.4 + - - +
125D VAL* 4.3 0.3 + - - -
126D LYS* 6.1 0.2 - - - +
260D THR* 5.1 2.3 - - - +
307D LYS* 3.6 12.5 + - - +
308D ILE* 1.3 76.4 - - - +
310D LEU* 1.3 61.0 + - - +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D VAL* 3.7 5.3 - - - +
47D THR* 2.9 82.5 + - + +
49D ILE* 4.1 12.1 - - + -
105D LEU* 3.8 19.7 - - + -
120D TRP* 4.0 14.6 - - + -
121D GLU 3.1 20.0 - - - +
122D ALA* 3.9 5.2 - - + +
123D VAL* 4.4 1.3 - - - +
278D LEU* 3.3 35.2 - - + -
308D ILE* 3.6 9.2 - - + +
309D THR* 1.3 77.6 - - - +
311D ARG* 1.3 59.0 + - - +
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Residues in contact with ARG 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PRO 5.6 0.4 - - - +
44D ASP* 5.2 9.2 - - - +
45D SER 4.6 4.0 - - - -
46D VAL* 5.0 6.1 - - + +
119D MET 3.8 0.3 - - - +
120D TRP* 3.6 11.6 - - - -
121D GLU* 2.7 82.8 + - + +
123D VAL* 4.2 16.2 - - + +
264D LEU* 4.4 11.7 - - - +
268D GLY 3.3 10.5 + - - -
310D LEU* 1.3 73.1 - - - +
312D LYS* 1.3 70.8 + - - +
313D ARG* 3.0 28.1 + - + +
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Residues in contact with LYS 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL* 4.0 8.9 - - - +
41D THR* 2.9 28.6 + - - -
42D GLY 2.5 37.3 + - - +
43D PRO* 3.0 27.7 + - + +
44D ASP 5.4 0.2 - - - -
45D SER* 3.3 23.6 + - - +
108D LEU* 3.6 35.0 - - + +
109D ASN* 4.0 13.1 + - - +
118D GLN* 4.1 12.9 - - - +
119D MET 4.1 2.7 - - - -
120D TRP* 4.0 18.4 - - + -
311D ARG* 1.3 79.6 - - - +
313D ARG* 1.3 60.4 + - - +
314D TRP* 4.2 3.6 + - - -
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Residues in contact with ARG 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PRO* 5.6 0.2 - - - +
23C ALA* 3.7 31.9 - - - +
118D GLN* 3.2 5.2 - - - -
119D MET* 2.5 49.4 + - - +
121D GLU* 2.6 38.8 + - + +
267D ASN 5.0 0.4 + - - -
268D GLY 2.3 32.5 + - - -
269D VAL* 3.2 16.6 - - - +
272D LEU* 4.8 7.7 - - + +
311D ARG* 3.0 16.7 + - - +
312D LYS* 1.3 75.6 - - - +
314D TRP* 1.3 87.4 + - + +
315D VAL* 3.6 10.1 - - + +
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Residues in contact with TRP 314 (chain D).
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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20C PRO* 3.8 32.0 - - + +
21C ARG 5.3 2.0 - - - -
22C PRO* 3.6 27.2 - - + +
23C ALA 4.7 0.2 + - - -
43D PRO* 5.5 6.0 - - + +
109D ASN* 4.1 9.9 - - + -
110D GLU* 4.2 15.3 - - - -
111D ASP* 4.7 3.1 - - + -
116D THR* 2.8 38.4 - - + +
117D LEU 2.9 34.3 - - - -
118D GLN* 3.4 35.1 + - + -
312D LYS 4.2 3.3 + - - -
313D ARG* 1.3 92.3 + - + +
315D VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PRO* 3.5 14.0 - - - +
116D THR* 3.3 10.2 + - - -
117D LEU* 2.7 42.4 + - + +
119D MET* 3.4 51.1 - - + -
272D LEU* 4.8 7.4 - - + -
313D ARG* 3.6 11.9 - - - +
314D TRP* 1.3 80.7 - - - +
316D LYS* 1.3 73.3 + - - +
317D ASN* 4.9 0.4 - - - -
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Residues in contact with LYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PRO* 3.9 15.0 - - + +
114D CYS 3.5 14.8 + - - -
115D ASP* 3.2 31.9 - - + +
116D THR* 5.1 0.7 - - - +
315D VAL* 1.3 84.2 - - - +
317D ASN* 1.3 78.5 + - - +
318D PRO* 2.8 17.8 - - + +
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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