Contacts of the strand formed by residues 303 - 316 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU 3.5 9.9 - - - +
54B ASN* 3.5 23.1 - - - +
55B PRO* 3.6 8.2 - - + -
129B VAL* 3.2 6.5 - - - +
130B VAL* 2.9 56.8 + - + +
301B GLY 4.8 0.2 - - - +
302B LEU* 1.3 89.7 - - + +
304B ARG* 1.3 62.8 + - - +
177C LEU* 4.0 3.8 - - + -
207C VAL* 3.3 21.5 - - - +
208C LEU* 4.1 14.6 - - + -
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 2.9 8.0 - - - +
53B LEU 2.9 37.4 + - - -
127B THR* 2.9 27.0 + - - +
128B GLU* 3.4 7.1 - - - +
129B VAL* 3.6 11.7 - - + +
130B VAL* 5.3 0.9 - - - -
163B HIS* 4.5 8.1 - - - +
164B VAL 4.2 4.2 + - - +
165B PHE* 3.1 38.8 - - - -
282B CYS* 3.7 18.7 - - - +
284B ASP* 2.7 55.5 + - - +
303B PRO* 1.3 76.8 - - - +
305B TYR* 1.3 58.1 + - - +
306B PHE* 3.1 31.7 - - + -
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Residues in contact with TYR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU* 2.9 39.5 + - + +
51B ALA 3.5 10.1 - - - -
52B PHE* 3.9 5.6 - - + -
126B LYS* 3.9 13.7 - - + -
127B THR* 2.6 36.0 + - - -
128B GLU* 2.7 20.9 + - + +
130B VAL* 4.8 4.9 - - + +
304B ARG* 1.3 68.5 - - - +
306B PHE* 1.3 85.4 + - - +
307B LYS* 3.4 30.0 - - + +
231C PRO* 2.8 53.0 - - + +
232C ALA 3.4 12.8 + - - -
233C LYS 4.4 0.3 + - - -
349F GLU* 5.6 7.2 - - + -
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE 3.2 1.0 - - - +
50B GLU* 2.9 26.7 - - - +
51B ALA* 2.7 15.7 + - - +
52B PHE* 3.8 7.6 - - - -
53B LEU* 3.6 27.8 - - + -
125B VAL* 4.5 10.3 - - + -
126B LYS 3.5 3.8 - - - -
127B THR* 4.6 2.7 - - - -
165B PHE* 4.4 17.9 - + - -
166B ALA 4.5 4.0 - - - -
167B VAL* 4.6 1.6 - - + -
280B LEU* 3.6 37.0 - - + -
281B SER 4.7 0.7 - - - -
282B CYS* 4.1 6.3 - - + -
304B ARG* 3.1 51.6 - - + -
305B TYR* 1.3 93.1 - - - +
307B LYS* 1.3 60.1 + - - +
308B ILE* 3.4 15.0 - - + -
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU* 3.1 42.8 + - + +
49B ILE 3.4 4.5 - - - +
50B GLU* 3.7 23.6 - - + +
124B SER 3.7 0.3 - - - +
125B VAL* 2.9 23.8 - - - -
126B LYS* 2.7 43.3 + - + +
260B THR* 5.2 1.2 - - + +
305B TYR* 3.4 22.4 + - + +
306B PHE* 1.3 74.1 - - - +
308B ILE* 1.3 62.7 + - - +
309B THR* 3.7 6.2 + - + +
233C LYS 4.4 7.6 + - - -
266C GLU* 4.2 20.5 + - - +
352F ARG* 5.4 0.4 - - - +
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Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B THR 3.5 4.9 - - - +
48B GLU* 3.5 1.8 - - - -
49B ILE* 2.9 42.4 + - + +
51B ALA* 5.7 0.7 - - + +
103B LEU* 6.5 0.2 - - + -
122B ALA* 3.8 18.8 - - + -
124B SER 3.7 6.3 - - - +
125B VAL* 4.0 14.4 - - + -
167B VAL* 4.9 2.9 - - + -
263B LEU* 4.5 1.8 - - + -
278B LEU* 3.9 20.2 - - + -
280B LEU* 4.0 20.9 - - + -
306B PHE* 3.4 31.9 - - + -
307B LYS* 1.3 76.0 - - - +
309B THR* 1.3 63.4 + - - +
310B LEU* 3.7 28.3 + - + +
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 4.6 11.4 - - + -
47B THR 3.6 4.0 - - - +
48B GLU* 3.7 30.7 - - + +
122B ALA* 3.6 0.7 - - - -
123B VAL* 2.7 38.6 + - - +
124B SER* 2.7 35.2 + - - +
125B VAL 4.1 0.3 + - - -
260B THR* 4.7 4.2 - - - +
307B LYS* 3.7 7.8 + - + +
308B ILE* 1.3 72.1 - - - +
310B LEU* 1.3 55.3 + - - +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 3.0 20.4 - - - +
47B THR* 3.4 35.5 + - + +
49B ILE* 4.5 9.0 - - + -
105B LEU* 4.2 18.6 - - + -
120B TRP* 4.2 12.8 - - + -
121B GLU 2.9 26.5 - - - +
122B ALA* 3.4 6.5 - - + +
123B VAL* 4.2 1.3 - - - -
273B CYS* 4.8 5.4 - - - -
278B LEU* 4.0 22.0 - - + -
308B ILE* 3.7 24.2 - - + +
309B THR* 1.3 76.2 - - - +
311B ARG* 1.3 58.2 + - - +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASP* 4.9 8.1 - - - +
45B SER 5.1 0.4 - - - -
46B VAL* 4.4 14.1 - - + +
119B MET 3.5 1.9 - - - +
120B TRP* 3.6 7.8 - - - -
121B GLU* 2.8 61.2 + - + +
123B VAL* 4.0 16.2 - - + +
264B LEU* 4.0 15.9 - - - +
268B GLY 3.5 8.3 + - - -
310B LEU* 1.3 74.1 - - - +
312B LYS* 1.3 71.7 + - - +
313B ARG* 2.8 36.8 + - - +
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 5.6 0.4 - - - +
41B THR* 2.6 36.6 + - - +
42B GLY 2.6 31.4 + - - +
43B PRO* 3.5 29.3 + - + +
44B ASP* 5.2 1.2 + - - +
45B SER* 3.8 9.6 + - - +
108B LEU* 3.9 17.6 - - + +
109B ASN* 5.9 0.4 + - - -
118B GLN* 4.1 25.0 - - - +
119B MET 3.7 4.7 - - - -
120B TRP* 3.7 26.7 - - + -
311B ARG* 1.3 81.7 - - - +
313B ARG* 1.3 60.0 - - - +
314B TRP* 4.1 4.2 + - - -
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Residues in contact with ARG 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO* 5.8 0.2 - - - -
23A ALA* 3.3 34.0 - - - +
118B GLN* 3.0 6.3 - - - -
119B MET* 2.8 38.5 + - - +
121B GLU* 2.6 45.1 + - + +
268B GLY 2.5 29.9 + - - -
269B VAL* 3.1 24.3 - - - +
272B LEU* 4.9 4.1 - - + +
311B ARG* 2.8 16.6 + - - +
312B LYS* 1.3 75.5 - - - +
314B TRP* 1.3 80.0 + - + +
315B VAL* 3.3 17.7 - - + +
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Residues in contact with TRP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO* 4.0 30.1 - - + +
21A ARG 5.5 0.7 - - - -
22A PRO* 3.3 26.1 - - + +
43B PRO* 5.6 5.5 - - + +
109B ASN* 4.1 15.0 - - + -
110B GLU 4.4 11.2 - - - -
111B ASP* 4.5 2.5 - - + -
116B THR* 3.2 28.5 - - + -
117B LEU* 3.1 48.9 - - - -
118B GLN* 3.4 29.4 + - + -
312B LYS 4.1 3.8 + - - -
313B ARG* 1.3 87.2 - - + +
315B VAL* 1.3 59.7 - - - +
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO* 3.3 10.3 - - + -
116B THR* 2.8 15.6 + - - -
117B LEU* 2.6 52.0 + - + +
119B MET* 3.9 18.4 - - + -
272B LEU* 4.3 19.1 - - + -
313B ARG* 3.3 26.9 - - - +
314B TRP* 1.3 80.8 - - - +
316B LYS* 1.3 66.4 + - - +
318B PRO* 5.4 2.0 - - + -
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO 5.6 1.0 + - - -
22A PRO* 3.2 23.8 - - + +
114B CYS* 2.8 27.1 + - - +
115B ASP* 3.1 17.7 + - - +
116B THR* 3.7 13.1 + - - -
315B VAL* 1.3 81.1 - - - +
317B ASN* 1.3 84.6 + - - +
318B PRO* 3.2 5.0 - - - +
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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