Contacts of the strand formed by residues 303 - 316 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU 3.3 16.4 - - - +
54A ASN* 3.8 18.4 - - - +
55A PRO* 3.7 5.6 - - + -
129A VAL* 3.2 8.0 - - - +
130A VAL* 3.1 53.5 + - + +
302A LEU* 1.3 97.1 - - + +
304A ARG* 1.3 62.5 + - - +
177B LEU* 3.8 2.5 - - + -
207B VAL* 3.4 22.0 - - + +
208B LEU* 4.0 12.6 - - + -
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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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52A PHE* 2.9 28.3 - - - -
53A LEU 2.9 16.6 + - - +
127A THR* 2.9 25.5 + - - +
128A GLU* 3.3 8.9 - - - +
129A VAL* 3.4 17.6 - - + +
130A VAL* 4.8 1.1 - - - -
163A HIS* 5.1 5.1 - - - +
164A VAL 3.9 9.5 + - - +
165A PHE* 3.6 32.3 - - - -
282A CYS* 3.8 14.1 - - - -
284A ASP* 2.6 49.0 + - - +
303A PRO* 1.3 77.9 - - - +
305A TYR* 1.3 57.8 + - - +
306A PHE* 3.0 40.6 - - + -
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Residues in contact with TYR 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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50A GLU* 2.8 43.7 + - + +
51A ALA 3.4 10.5 - - - -
52A PHE* 4.2 5.2 - - + -
126A LYS* 4.1 12.8 - - + -
127A THR* 2.8 34.4 + - - -
128A GLU* 2.7 18.6 + - + +
130A VAL* 4.9 3.8 - - + +
304A ARG* 1.3 68.5 - - - +
306A PHE* 1.3 78.0 + - - +
307A LYS* 3.5 28.9 - - + +
208B LEU* 6.1 0.2 - - - +
231B PRO* 2.8 53.2 - - + -
232B ALA 3.5 4.9 + - - -
233B LYS* 3.4 11.2 - - - -
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Residues in contact with PHE 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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49A ILE 3.1 0.7 - - - +
50A GLU* 2.8 27.5 - - - +
51A ALA 2.7 20.3 + - - +
52A PHE* 4.2 3.4 - - - -
53A LEU* 4.0 25.6 - - + -
125A VAL* 4.5 9.4 - - + -
126A LYS 3.5 4.3 - - - -
127A THR* 4.6 2.2 - - - -
165A PHE* 4.3 18.2 - + - -
166A ALA 4.5 4.5 - - - -
167A VAL* 5.0 3.6 - - + -
280A LEU* 3.5 35.4 - - + -
281A SER 4.6 0.9 - - - -
282A CYS* 4.4 6.7 - - + -
304A ARG* 3.0 52.5 - - + -
305A TYR* 1.3 95.7 - - - +
307A LYS* 1.3 62.3 + - - +
308A ILE* 3.2 18.6 - - + -
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Residues in contact with LYS 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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48A GLU* 3.0 43.4 + - + -
49A ILE 3.3 4.3 - - - +
50A GLU* 3.8 25.1 - - + -
125A VAL* 2.9 25.6 - - - -
126A LYS* 2.8 47.8 + - + +
305A TYR* 3.5 23.8 - - + +
306A PHE* 1.3 75.2 - - - +
308A ILE* 1.3 61.1 + - - +
309A THR* 3.6 5.7 + - - +
233B LYS 4.7 5.1 + - - -
266B GLU* 4.6 11.3 + - - -
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Residues in contact with ILE 308 (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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47A THR 3.3 7.1 - - - +
48A GLU* 3.5 1.5 - - - -
49A ILE* 2.8 38.8 + - + +
51A ALA* 5.6 0.4 - - + +
122A ALA* 4.5 11.4 - - + -
124A SER 3.7 5.2 - - - +
125A VAL* 3.8 13.5 - - + -
167A VAL* 4.4 7.6 - - + -
263A LEU* 4.9 0.9 - - + -
278A LEU* 3.7 27.8 - - + -
280A LEU* 3.8 18.4 - - + -
306A PHE* 3.2 36.1 - - + -
307A LYS* 1.3 74.5 - - - +
309A THR* 1.3 65.1 + - - +
310A LEU* 3.5 25.7 - - + +
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Residues in contact with THR 309 (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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46A VAL* 4.8 11.2 - - + -
47A THR 3.6 2.5 - - - -
48A GLU* 4.5 21.4 - - + +
122A ALA* 3.9 0.7 - - - -
123A VAL* 2.7 30.2 + - + +
124A SER* 3.0 37.6 + - - +
125A VAL* 4.0 0.9 + - - -
126A LYS* 6.1 0.2 - - - +
260A THR* 4.6 5.4 - - - +
307A LYS* 3.8 8.8 + - - +
308A ILE* 1.3 72.9 - - - +
310A LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 310 (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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46A VAL* 3.5 5.8 - - - +
47A THR* 3.0 50.9 + - - +
49A ILE* 4.2 15.5 - - + -
105A LEU* 3.7 19.1 - - + -
120A TRP* 3.4 35.5 - - + -
121A GLU 2.8 18.2 - - - +
122A ALA* 3.4 11.9 - - + -
123A VAL* 4.1 2.7 - - - +
273A CYS* 5.8 1.6 - - - -
278A LEU* 5.2 4.3 - - + -
308A ILE* 3.5 25.1 - - + +
309A THR* 1.3 77.2 - - - +
311A ARG* 1.3 57.4 + - - +
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Residues in contact with ARG 311 (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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44A ASP* 5.9 1.1 - - - +
45A SER 4.3 13.7 - - - +
46A VAL* 4.9 5.6 - - + -
120A TRP* 3.6 7.3 - - - -
121A GLU* 2.7 82.0 + - + +
123A VAL* 4.0 14.2 - - + +
264A LEU* 4.1 11.6 - - - +
268A GLY 2.9 23.8 + - - -
310A LEU* 1.3 72.9 - - - +
312A LYS* 1.3 72.4 + - - +
313A ARG* 3.5 14.8 - - - +
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Residues in contact with LYS 312 (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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41A THR* 2.9 25.0 + - - +
42A GLY 2.5 33.6 + - - +
43A PRO 3.2 24.0 + - - +
45A SER* 3.1 18.8 + - - +
108A LEU* 4.3 16.1 + - + +
118A GLN* 3.7 31.7 - - + +
119A MET 3.7 4.7 - - - +
120A TRP* 3.7 26.7 - - + -
311A ARG* 1.3 82.5 - - - +
313A ARG* 1.3 61.9 + - - +
314A TRP* 4.2 5.4 + - - -
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Residues in contact with ARG 313 (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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118A GLN* 3.3 5.7 - - - +
119A MET* 2.7 44.6 + - + +
121A GLU* 2.7 34.7 + - + +
267A ASN 4.1 4.2 + - - -
268A GLY 2.6 29.3 + - - -
269A VAL* 3.5 20.5 - - - +
272A LEU* 4.4 13.2 - - + -
311A ARG* 3.5 12.2 + - - +
312A LYS* 1.3 75.9 - - - +
314A TRP* 1.3 81.0 + - - +
315A VAL* 4.2 3.5 - - + +
23E ALA* 2.8 33.9 - - + +
24E PRO* 5.0 3.8 + - - +
25E VAL* 4.2 11.5 - - - +
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Residues in contact with TRP 314 (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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43A PRO* 5.1 11.6 - - + +
44A ASP* 5.9 0.6 + - - -
109A ASN* 5.3 2.5 - - - -
116A THR* 3.5 24.7 - - + -
117A LEU 3.1 25.8 - - - -
118A GLN* 3.4 45.3 + - + -
312A LYS 5.1 5.6 + - - -
313A ARG* 1.3 79.7 - - - +
315A VAL* 1.3 69.1 + - - +
19E CYS* 5.9 1.3 - - + -
20E PRO* 3.9 38.5 - - + +
21E ARG 5.4 2.2 - - - -
22E PRO* 3.8 20.0 - - + -
23E ALA* 3.4 24.1 + - + +
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Residues in contact with VAL 315 (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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116A THR* 2.9 12.6 + - - +
117A LEU* 2.9 40.9 + - + +
118A GLN 4.8 0.2 - - - -
119A MET* 3.8 35.4 - - + +
313A ARG* 4.2 8.5 - - + +
314A TRP* 1.3 82.4 - - - +
316A LYS* 1.3 71.8 + - + +
22E PRO* 3.9 12.5 - - + +
23E ALA* 6.0 2.2 - - + +
25E VAL* 6.1 5.4 - - + -
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Residues in contact with LYS 316 (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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115A ASP* 3.1 23.7 + - + +
117A LEU* 4.7 2.4 - - - +
315A VAL* 1.3 87.0 - - + +
317A ASN* 1.3 91.3 + - - +
318A PRO* 3.1 19.4 - - - +
320A PRO* 3.1 18.7 - - - +
321A MET* 4.9 12.5 - - - -
22E PRO* 4.5 10.2 - - + +
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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